R-universe search: polyadenylation site

ropensci

beautier:'BEAUti' from R

'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAUti 2' (which is part of 'BEAST2') is a GUI tool that allows users to specify the many possible setups and generates the XML file 'BEAST2' needs to run. This package provides a way to create 'BEAST2' input files without active user input, but using R function calls instead.

Maintained by Richèl J.C. Bilderbeek. Last updated 23 days ago.

bayesian beast beast2 beauti phylogenetic-inference phylogenetics

98.2 match 13 stars 8.76 score 198 scripts 5 dependents

neotomadb

neotoma2:Working with the Neotoma Paleoecology Database

Access and manipulation of data using the Neotoma Paleoecology Database. <https://api.neotomadb.org/api-docs/>.

Maintained by Dominguez Vidana Socorro. Last updated 8 months ago.

earthcube neotoma nsf paleoecology

109.1 match 8 stars 5.35 score 56 scripts

bioc

BindingSiteFinder:Binding site defintion based on iCLIP data

Precise knowledge on the binding sites of an RNA-binding protein (RBP) is key to understand (post-) transcriptional regulatory processes. Here we present a workflow that describes how exact binding sites can be defined from iCLIP data. The package provides functions for binding site definition and result visualization. For details please see the vignette.

Maintained by Mirko Brüggemann. Last updated 4 months ago.

sequencing geneexpression generegulation functionalgenomics coverage dataimport binding-site-classification binding-sites bioconductor-package iclip rna-binding-proteins

83.2 match 6 stars 5.65 score 3 scripts

ncss-tech

aqp:Algorithms for Quantitative Pedology

The Algorithms for Quantitative Pedology (AQP) project was started in 2009 to organize a loosely-related set of concepts and source code on the topic of soil profile visualization, aggregation, and classification into this package (aqp). Over the past 8 years, the project has grown into a suite of related R packages that enhance and simplify the quantitative analysis of soil profile data. Central to the AQP project is a new vocabulary of specialized functions and data structures that can accommodate the inherent complexity of soil profile information; freeing the scientist to focus on ideas rather than boilerplate data processing tasks <doi:10.1016/j.cageo.2012.10.020>. These functions and data structures have been extensively tested and documented, applied to projects involving hundreds of thousands of soil profiles, and deeply integrated into widely used tools such as SoilWeb <https://casoilresource.lawr.ucdavis.edu/soilweb-apps>. Components of the AQP project (aqp, soilDB, sharpshootR, soilReports packages) serve an important role in routine data analysis within the USDA-NRCS Soil Science Division. The AQP suite of R packages offer a convenient platform for bridging the gap between pedometric theory and practice.

Maintained by Dylan Beaudette. Last updated 29 days ago.

digital-soil-mapping ncss-tech nrcs pedology pedometrics soil soil-survey usda

30.3 match 55 stars 11.77 score 1.2k scripts 2 dependents

r-lib

pkgdown:Make Static HTML Documentation for a Package

Generate an attractive and useful website from a source package. 'pkgdown' converts your documentation, vignettes, 'README', and more to 'HTML' making it easy to share information about your package online.

Maintained by Hadley Wickham. Last updated 10 hours ago.

documentation-tool

18.4 match 734 stars 18.47 score 588 scripts 162 dependents

frbcesab

funbiogeo:Functional Biogeography Analyses

Helps users with analyses in functional biogeogeography by loading and combining data, computing trait coverage, as well as computing functional diversity indices, drawing maps, correlating them with the environment, and upscaling assemblages.

Maintained by Nicolas Casajus. Last updated 4 days ago.

functional-biogeography functional-diversity functional-trait

58.9 match 11 stars 5.60 score 8 scripts

bioc

RnBeads:RnBeads

RnBeads facilitates comprehensive analysis of various types of DNA methylation data at the genome scale.

Maintained by Fabian Mueller. Last updated 1 months ago.

dnamethylation methylationarray methylseq epigenetics qualitycontrol preprocessing batcheffect differentialmethylation sequencing cpgisland immunooncology twochannel dataimport

38.3 match 6.85 score 169 scripts 1 dependents

kwstat

agridat:Agricultural Datasets

Datasets from books, papers, and websites related to agriculture. Example graphics and analyses are included. Data come from small-plot trials, multi-environment trials, uniformity trials, yield monitors, and more.

Maintained by Kevin Wright. Last updated 28 days ago.

data

21.6 match 125 stars 11.02 score 1.7k scripts 2 dependents

sebastien-plutniak

archeofrag:Spatial Analysis in Archaeology from Refitting Fragments

Methods to analyse spatial units in archaeology from the relationships between refitting fragmented objects scattered in these units (e.g. stratigraphic layers). Graphs are used to model archaeological observations. The package is mainly based on the 'igraph' package for graph analysis. Functions can: 1) create, manipulate, and simulate fragmentation graphs, 2) measure the cohesion and admixture of archaeological spatial units, and 3) characterise the topology of a specific set of refitting relationships. Empirical datasets are provided as examples. Documentation about 'archeofrag' is provided by the vignette included in this package, by the accompanying scientific papers: Plutniak (2021, Journal of Archaeological Science, <doi:10.1016/j.jas.2021.105501>) and Plutniak (2022, Journal of Open Source Software, <doi:10.21105/joss.04335>). This package is complemented by a companion GUI application available at <https://analytics.huma-num.fr/Sebastien.Plutniak/archeofrag/>.

Maintained by Sebastien Plutniak. Last updated 7 hours ago.

archaeological-objects archaeological-science archaeology fragmentation network-analysis

35.2 match 20 stars 6.38 score 10 scripts 1 dependents

doi-usgs

dataRetrieval:Retrieval Functions for USGS and EPA Hydrology and Water Quality Data

Collection of functions to help retrieve U.S. Geological Survey and U.S. Environmental Protection Agency water quality and hydrology data from web services. Data are discovered from National Water Information System <https://waterservices.usgs.gov/> and <https://waterdata.usgs.gov/nwis>. Water quality data are obtained from the Water Quality Portal <https://www.waterqualitydata.us/>.

Maintained by Laura DeCicco. Last updated 18 days ago.

usgs

13.4 match 280 stars 14.18 score 1.7k scripts 15 dependents

emf-creaf

indicspecies:Relationship Between Species and Groups of Sites

Functions to assess the strength and statistical significance of the relationship between species occurrence/abundance and groups of sites [De Caceres & Legendre (2009) <doi:10.1890/08-1823.1>]. Also includes functions to measure species niche breadth using resource categories [De Caceres et al. (2011) <doi:10.1111/J.1600-0706.2011.19679.x>].

Maintained by Miquel De Cáceres. Last updated 24 days ago.

19.8 match 10 stars 9.49 score 386 scripts 4 dependents

sapfluxnet

sapfluxnetr:Working with 'Sapfluxnet' Project Data

Access, modify, aggregate and plot data from the 'Sapfluxnet' project (<http://sapfluxnet.creaf.cat>), the first global database of sap flow measurements.

Maintained by Victor Granda. Last updated 2 years ago.

28.4 match 25 stars 6.57 score 49 scripts

bioc

InPAS:Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

Alternative polyadenylation (APA) is one of the important post- transcriptional regulation mechanisms which occurs in most human genes. InPAS facilitates the discovery of novel APA sites and the differential usage of APA sites from RNA-Seq data. It leverages cleanUpdTSeq to fine tune identified APA sites by removing false sites.

Maintained by Jianhong Ou. Last updated 2 months ago.

alternative polyadenylation differential polyadenylation site usage rna-seq gene regulation transcription

42.9 match 4.30 score 1 scripts

adeverse

ade4:Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>.

Maintained by Aurélie Siberchicot. Last updated 13 days ago.

openblas cpp

12.0 match 39 stars 14.96 score 2.2k scripts 256 dependents

bioc

sitePath:Phylogeny-based sequence clustering with site polymorphism

Using site polymorphism is one of the ways to cluster DNA/protein sequences but it is possible for the sequences with the same polymorphism on a single site to be genetically distant. This package is aimed at clustering sequences using site polymorphism and their corresponding phylogenetic trees. By considering their location on the tree, only the structurally adjacent sequences will be clustered. However, the adjacent sequences may not necessarily have the same polymorphism. So a branch-and-bound like algorithm is used to minimize the entropy representing the purity of site polymorphism of each cluster.

Maintained by Chengyang Ji. Last updated 5 months ago.

alignment multiplesequencealignment phylogenetics snp software mutation cpp

33.7 match 8 stars 5.20 score 9 scripts

alanarnholt

BSDA:Basic Statistics and Data Analysis

Data sets for book "Basic Statistics and Data Analysis" by Larry J. Kitchens.

Maintained by Alan T. Arnholt. Last updated 2 years ago.

17.0 match 7 stars 9.11 score 1.3k scripts 6 dependents

bioc

consensusSeekeR:Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges

This package compares genomic positions and genomic ranges from multiple experiments to extract common regions. The size of the analyzed region is adjustable as well as the number of experiences in which a feature must be present in a potential region to tag this region as a consensus region. In genomic analysis where feature identification generates a position value surrounded by a genomic range, such as ChIP-Seq peaks and nucleosome positions, the replication of an experiment may result in slight differences between predicted values. This package enables the conciliation of the results into consensus regions.

Maintained by Astrid Deschênes. Last updated 5 months ago.

biologicalquestion chipseq genetics multiplecomparison transcription peakdetection sequencing coverage chip-seq-analysis genomic-data-analysis nucleosome-positioning

29.2 match 1 stars 5.26 score 5 scripts 1 dependents

kjhealy

gssrdoc:Document General Social Survey Variable

The General Social Survey (GSS) is a long-running, mostly annual survey of US households. It is administered by the National Opinion Research Center (NORC). This package contains the a tibble with information on the survey variables, together with every variable documented as an R help page. For more information on the GSS see \url{http://gss.norc.org}.

Maintained by Kieran Healy. Last updated 11 months ago.

67.1 match 2.28 score 38 scripts

ncss-tech

soilDB:Soil Database Interface

A collection of functions for reading soil data from U.S. Department of Agriculture Natural Resources Conservation Service (USDA-NRCS) and National Cooperative Soil Survey (NCSS) databases.

Maintained by Andrew Brown. Last updated 7 days ago.

kssl nasis nrcs soil soil-data-access soil-survey soilweb sql usda

13.5 match 87 stars 11.34 score 1.0k scripts 1 dependents

ropensci

neotoma:Access to the Neotoma Paleoecological Database Through R

NOTE: This package is deprecated. Please use the neotoma2 package described at https://github.com/NeotomaDB/neotoma2. Access paleoecological datasets from the Neotoma Paleoecological Database using the published API (<http://wnapi.neotomadb.org/>), only containing datasets uploaded prior to June 2020. The functions in this package access various pre-built API functions and attempt to return the results from Neotoma in a usable format for researchers and the public.

Maintained by Simon J. Goring. Last updated 2 years ago.

neotoma neotoma-apis neotoma-database nsf paleoecology

29.9 match 30 stars 5.04 score 145 scripts

bnaras

homomorpheR:Homomorphic Computations in R

Homomorphic computations in R for privacy-preserving applications. Currently only the Paillier Scheme is implemented.

Maintained by Balasubramanian Narasimhan. Last updated 3 years ago.

24.2 match 4 stars 5.73 score 18 scripts 1 dependents

ropensci

epair:EPA Data Helper for R

Aid the user in making queries to the EPA API site found at https://aqs.epa.gov/aqsweb/documents/data_api. This package combines API calling methods from various web scraping packages with specific strings to retrieve data from the EPA API. It also contains easy to use loaded variables that help a user navigate services offered by the API and aid the user in determining the appropriate way to make a an API call.

Maintained by G.L. Orozco-Mulfinger. Last updated 3 years ago.

28.3 match 7 stars 4.89 score 11 scripts

workflowr

workflowr:A Framework for Reproducible and Collaborative Data Science

Provides a workflow for your analysis projects by combining literate programming ('knitr' and 'rmarkdown') and version control ('Git', via 'git2r') to generate a website containing time-stamped, versioned, and documented results.

Maintained by John Blischak. Last updated 4 months ago.

git project-management rmarkdown website workflow

11.6 match 845 stars 11.83 score 566 scripts

smbc-nzp

MigConnectivity:Estimate Migratory Connectivity for Migratory Animals

Allows the user to estimate transition probabilities for migratory animals between any two phases of the annual cycle, using a variety of different data types. Also quantifies the strength of migratory connectivity (MC), a standardized metric to quantify the extent to which populations co-occur between two phases of the annual cycle. Includes functions to estimate MC and the more traditional metric of migratory connectivity strength (Mantel correlation) incorporating uncertainty from multiple sources of sampling error. For cross-species comparisons, methods are provided to estimate differences in migratory connectivity strength, incorporating uncertainty. See Cohen et al. (2018) <doi:10.1111/2041-210X.12916>, Cohen et al. (2019) <doi:10.1111/ecog.03974>, and Roberts et al. (2023) <doi:10.1002/eap.2788> for details on some of these methods.

Maintained by Jeffrey A. Hostetler. Last updated 12 months ago.

jags cpp

20.0 match 8 stars 6.77 score 41 scripts

pecanproject

PEcAn.settings:PEcAn Settings package

Contains functions to read PEcAn settings files.

Maintained by David LeBauer. Last updated 2 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants

12.9 match 216 stars 10.00 score 54 scripts 17 dependents

bioc

cleanUpdTSeq:cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending data

This package implements a Naive Bayes classifier for accurately differentiating true polyadenylation sites (pA sites) from oligo(dT)-mediated 3' end sequencing such as PAS-Seq, PolyA-Seq and RNA-Seq by filtering out false polyadenylation sites, mainly due to oligo(dT)-mediated internal priming during reverse transcription. The classifer is highly accurate and outperforms other heuristic methods.

Maintained by Jianhong Ou. Last updated 2 months ago.

sequencing 3 end sequencing polyadenylation site internal priming

29.7 match 4.26 score 8 scripts 1 dependents

bioc

ORFik:Open Reading Frames in Genomics

R package for analysis of transcript and translation features through manipulation of sequence data and NGS data like Ribo-Seq, RNA-Seq, TCP-Seq and CAGE. It is generalized in the sense that any transcript region can be analysed, as the name hints to it was made with investigation of ribosomal patterns over Open Reading Frames (ORFs) as it's primary use case. ORFik is extremely fast through use of C++, data.table and GenomicRanges. Package allows to reassign starts of the transcripts with the use of CAGE-Seq data, automatic shifting of RiboSeq reads, finding of Open Reading Frames for whole genomes and much more.

Maintained by Haakon Tjeldnes. Last updated 28 days ago.

immunooncology software sequencing riboseq rnaseq functionalgenomics coverage alignment dataimport cpp

11.8 match 33 stars 10.63 score 115 scripts 2 dependents

pschmidtwalter

LWFBrook90R:Simulate Evapotranspiration and Soil Moisture with the SVAT Model LWF-Brook90

Provides a flexible and easy-to use interface for the soil vegetation atmosphere transport (SVAT) model LWF-BROOK90, written in Fortran. The model simulates daily transpiration, interception, soil and snow evaporation, streamflow and soil water fluxes through a soil profile covered with vegetation, as described in Hammel & Kennel (2001, ISBN:978-3-933506-16-0) and Federer et al. (2003) <doi:10.1175/1525-7541(2003)004%3C1276:SOAETS%3E2.0.CO;2>. A set of high-level functions for model set up, execution and parallelization provides easy access to plot-level SVAT simulations, as well as multi-run and large-scale applications.

Maintained by Paul Schmidt-Walter. Last updated 5 months ago.

evapotranspiration modeling waterbalance waterflux fortran

19.3 match 11 stars 6.38 score 27 scripts

bioc

ChIPpeakAnno:Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

The package encompasses a range of functions for identifying the closest gene, exon, miRNA, or custom features—such as highly conserved elements and user-supplied transcription factor binding sites. Additionally, users can retrieve sequences around the peaks and obtain enriched Gene Ontology (GO) or Pathway terms. In version 2.0.5 and beyond, new functionalities have been introduced. These include features for identifying peaks associated with bi-directional promoters along with summary statistics (peaksNearBDP), summarizing motif occurrences in peaks (summarizePatternInPeaks), and associating additional identifiers with annotated peaks or enrichedGO (addGeneIDs). The package integrates with various other packages such as biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest, and stat to enhance its analytical capabilities.

Maintained by Jianhong Ou. Last updated 2 months ago.

annotation chipseq chipchip

13.9 match 8.75 score 584 scripts 6 dependents

usepa

spsurvey:Spatial Sampling Design and Analysis

A design-based approach to statistical inference, with a focus on spatial data. Spatially balanced samples are selected using the Generalized Random Tessellation Stratified (GRTS) algorithm. The GRTS algorithm can be applied to finite resources (point geometries) and infinite resources (linear / linestring and areal / polygon geometries) and flexibly accommodates a diverse set of sampling design features, including stratification, unequal inclusion probabilities, proportional (to size) inclusion probabilities, legacy (historical) sites, a minimum distance between sites, and two options for replacement sites (reverse hierarchical order and nearest neighbor). Data are analyzed using a wide range of analysis functions that perform categorical variable analysis, continuous variable analysis, attributable risk analysis, risk difference analysis, relative risk analysis, change analysis, and trend analysis. spsurvey can also be used to summarize objects, visualize objects, select samples that are not spatially balanced, select panel samples, measure the amount of spatial balance in a sample, adjust design weights, and more. For additional details, see Dumelle et al. (2023) <doi:10.18637/jss.v105.i03>.

Maintained by Michael Dumelle. Last updated 7 months ago.

ord

13.4 match 15 stars 8.98 score 241 scripts 1 dependents

bioc

methodical:Discovering genomic regions where methylation is strongly associated with transcriptional activity

DNA methylation is generally considered to be associated with transcriptional silencing. However, comprehensive, genome-wide investigation of this relationship requires the evaluation of potentially millions of correlation values between the methylation of individual genomic loci and expression of associated transcripts in a relatively large numbers of samples. Methodical makes this process quick and easy while keeping a low memory footprint. It also provides a novel method for identifying regions where a number of methylation sites are consistently strongly associated with transcriptional expression. In addition, Methodical enables housing DNA methylation data from diverse sources (e.g. WGBS, RRBS and methylation arrays) with a common framework, lifting over DNA methylation data between different genome builds and creating base-resolution plots of the association between DNA methylation and transcriptional activity at transcriptional start sites.

Maintained by Richard Heery. Last updated 2 months ago.

dnamethylation methylationarray transcription genomewideassociation software openjdk

25.6 match 4.65 score 14 scripts

openpharma

simaerep:Find Clinical Trial Sites Under-Reporting Adverse Events

Monitoring of Adverse Event (AE) reporting in clinical trials is important for patient safety. Sites that are under-reporting AEs can be detected using Bootstrap-based simulations that simulate overall AE reporting. Based on the simulation an AE under-reporting probability is assigned to each site in a given trial (Koneswarakantha 2021 <doi:10.1007/s40264-020-01011-5>).

Maintained by Bjoern Koneswarakantha. Last updated 2 months ago.

ae-reporting clinical-trials

22.7 match 22 stars 5.22 score 25 scripts

bioc

crisprBase:Base functions and classes for CRISPR gRNA design

Provides S4 classes for general nucleases, CRISPR nucleases, CRISPR nickases, and base editors.Several CRISPR-specific genome arithmetic functions are implemented to help extract genomic coordinates of spacer and protospacer sequences. Commonly-used CRISPR nuclease objects are provided that can be readily used in other packages. Both DNA- and RNA-targeting nucleases are supported.

Maintained by Jean-Philippe Fortin. Last updated 5 months ago.

crispr functionalgenomics bioconductor bioconductor-package crispr-cas9 crispr-design crispr-target grna grna-sequence grna-sequences

16.5 match 5 stars 7.15 score 52 scripts 6 dependents

ropensci

allodb:Tree Biomass Estimation at Extra-Tropical Forest Plots

Standardize and simplify the tree biomass estimation process across globally distributed extratropical forests.

Maintained by Erika Gonzalez-Akre. Last updated 10 days ago.

19.5 match 38 stars 5.94 score 38 scripts

bioc

raer:RNA editing tools in R

Toolkit for identification and statistical testing of RNA editing signals from within R. Provides support for identifying sites from bulk-RNA and single cell RNA-seq datasets, and general methods for extraction of allelic read counts from alignment files. Facilitates annotation and exploratory analysis of editing signals using Bioconductor packages and resources.

Maintained by Kent Riemondy. Last updated 5 months ago.

multiplecomparison rnaseq singlecell sequencing coverage epitranscriptomics featureextraction annotation alignment bioconductor-package rna-seq-analysis single-cell-analysis single-cell-rna-seq curl bzip2 xz-utils zlib

19.2 match 8 stars 5.98 score 6 scripts

fcharte

mldr.datasets:R Ultimate Multilabel Dataset Repository

Large collection of multilabel datasets along with the functions needed to export them to several formats, to make partitions, and to obtain bibliographic information.

Maintained by David Charte. Last updated 6 years ago.

23.8 match 8 stars 4.68 score 120 scripts

pecanproject

PEcAn.data.atmosphere:PEcAn Functions Used for Managing Climate Driver Data

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The PECAn.data.atmosphere package converts climate driver data into a standard format for models integrated into PEcAn. As a standalone package, it provides an interface to access diverse climate data sets.

Maintained by David LeBauer. Last updated 2 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants

9.4 match 216 stars 11.59 score 64 scripts 14 dependents

bioc

SIMD:Statistical Inferences with MeDIP-seq Data (SIMD) to infer the methylation level for each CpG site

This package provides a inferential analysis method for detecting differentially expressed CpG sites in MeDIP-seq data. It uses statistical framework and EM algorithm, to identify differentially expressed CpG sites. The methods on this package are described in the article 'Methylation-level Inferences and Detection of Differential Methylation with Medip-seq Data' by Yan Zhou, Jiadi Zhu, Mingtao Zhao, Baoxue Zhang, Chunfu Jiang and Xiyan Yang (2018, pending publication).

Maintained by Jiadi Zhu. Last updated 5 months ago.

immunooncology differentialmethylation singlecell differentialexpression

21.4 match 5.00 score 2 scripts

jernejjevsenak

MLFS:Machine Learning Forest Simulator

Climate-sensitive forest simulator based on the principles of machine learning. It stimulates all key processes in the forest: radial growth, height growth, mortality, crown recession, regeneration and harvesting. The method for predicting tree heights was described by Skudnik and Jevšenak (2022) <doi:10.1016/j.foreco.2022.120017>, while the method for predicting basal area increments (BAI) was described by Jevšenak and Skudnik (2021) <doi:10.1016/j.foreco.2020.118601>.

Maintained by Jernej Jevsenak. Last updated 3 years ago.

30.2 match 2 stars 3.40 score 25 scripts

jmzobitz

neonSoilFlux:Compute Soil Carbon Fluxes for the National Ecological Observatory Network Sites

Acquires and synthesizes soil carbon fluxes at sites located in the National Ecological Observatory Network (NEON). Provides flux estimates and associated uncertainty as well as key environmental measurements (soil water, temperature, CO2 concentration) that are used to compute soil fluxes.

Maintained by John Zobitz. Last updated 10 months ago.

17.6 match 6 stars 5.43 score 2 scripts

carpentries

sandpaper:Create and Curate Carpentries Lessons

We provide tools to build a Carpentries-themed lesson repository into an accessible standalone static website. These include local tools and those designed to be used in a continuous integration context so that all the lesson author needs to focus on is writing the content of the actual lesson.

Maintained by Robert Davey. Last updated 2 months ago.

carpentries carpentries-infrastructure carpentries-workbench lesson-template lessons markdown static-site-generator

12.3 match 44 stars 7.72 score 8 scripts

ropensci

ReLTER:An Interface for the eLTER Community

ReLTER provides access to DEIMS-SDR (https://deims.org/), and allows interaction with data and software implemented by eLTER Research Infrastructure (RI) thus improving data sharing among European LTER projects. ReLTER uses the R language to access and interact with the DEIMS-SDR archive of information shared by the Long Term Ecological Research (LTER) network. This package grew within eLTER H2020 as a major project that will help advance the development of European Long-Term Ecosystem Research Infrastructures (eLTER RI - https://elter-ri.eu). The ReLTER package functions in particular allow to: - retrieve the information about entities (e.g. sites, datasets, and activities) shared by DEIMS-SDR (see e.g. get_site_info function); - interact with the [ODSEurope](maps.opendatascience.eu) starting with the dataset shared by [DEIMS-SDR](https://deims.org/) (see e.g. [get_site_ODS](https://docs.ropensci.org/ReLTER/reference/get_site_ODS.html) function); - use the eLTER site informations to download and crop geospatial data from other platforms (see e.g. get_site_ODS function); - improve the quality of the dataset (see e.g. get_id_worms). Functions currently implemented are derived from discussions of the needs among the eLTER users community. The ReLTER package will continue to follow the progress of eLTER-RI and evolve, adding new tools and improvements as required.

Maintained by Alessandro Oggioni. Last updated 1 years ago.

biodiversity-informatics data-science ecology elter research-infrastructure

26.3 match 12 stars 3.38 score 4 scripts

chuhousen

amerifluxr:Interface to 'AmeriFlux' Data Services

Programmatic interface to the 'AmeriFlux' database (<https://ameriflux.lbl.gov/>). Provide query, download, and data summary tools.

Maintained by Housen Chu. Last updated 2 months ago.

ameriflux api carbon-flux data time-series

10.5 match 22 stars 8.36 score 29 scripts 15 dependents

bioc

ISAnalytics:Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies

In gene therapy, stem cells are modified using viral vectors to deliver the therapeutic transgene and replace functional properties since the genetic modification is stable and inherited in all cell progeny. The retrieval and mapping of the sequences flanking the virus-host DNA junctions allows the identification of insertion sites (IS), essential for monitoring the evolution of genetically modified cells in vivo. A comprehensive toolkit for the analysis of IS is required to foster clonal trackign studies and supporting the assessment of safety and long term efficacy in vivo. This package is aimed at (1) supporting automation of IS workflow, (2) performing base and advance analysis for IS tracking (clonal abundance, clonal expansions and statistics for insertional mutagenesis, etc.), (3) providing basic biology insights of transduced stem cells in vivo.

Maintained by Francesco Gazzo. Last updated 3 months ago.

biomedicalinformatics sequencing singlecell

14.7 match 3 stars 5.83 score 15 scripts

bioc

Motif2Site:Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across conditions

Detect binding sites using motifs IUPAC sequence or bed coordinates and ChIP-seq experiments in bed or bam format. Combine/compare binding sites across experiments, tissues, or conditions. All normalization and differential steps are done using TMM-GLM method. Signal decomposition is done by setting motifs as the centers of the mixture of normal distribution curves.

Maintained by Peyman Zarrineh. Last updated 5 months ago.

software sequencing chipseq differentialpeakcalling epigenetics sequencematching

21.1 match 4.00 score 3 scripts

funecology

fundiversity:Easy Computation of Functional Diversity Indices

Computes six functional diversity indices. These are namely, Functional Divergence (FDiv), Function Evenness (FEve), Functional Richness (FRic), Functional Richness intersections (FRic_intersect), Functional Dispersion (FDis), and Rao's entropy (Q) (reviewed in Villéger et al. 2008 <doi:10.1890/07-1206.1>). Provides efficient, modular, and parallel functions to compute functional diversity indices (Grenié & Gruson 2023 <doi:10.1111/ecog.06585>).

Maintained by Matthias Grenié. Last updated 8 months ago.

biodiversity biodiversity-indicators biodiversity-informatics functional-diversity functional-ecology functional-trait functional-traits trait trait-based traits

11.2 match 38 stars 7.34 score 38 scripts

bioc

ChIPseqR:Identifying Protein Binding Sites in High-Throughput Sequencing Data

ChIPseqR identifies protein binding sites from ChIP-seq and nucleosome positioning experiments. The model used to describe binding events was developed to locate nucleosomes but should flexible enough to handle other types of experiments as well.

Maintained by Peter Humburg. Last updated 5 months ago.

chipseq infrastructure

17.3 match 4.70 score 1 scripts

bioc

PhosR:A set of methods and tools for comprehensive analysis of phosphoproteomics data

PhosR is a package for the comprenhensive analysis of phosphoproteomic data. There are two major components to PhosR: processing and downstream analysis. PhosR consists of various processing tools for phosphoproteomics data including filtering, imputation, normalisation, and functional analysis for inferring active kinases and signalling pathways.

Maintained by Taiyun Kim. Last updated 5 months ago.

software researchfield proteomics

17.2 match 4.71 score 51 scripts

cran

VCA:Variance Component Analysis

ANOVA and REML estimation of linear mixed models is implemented, once following Searle et al. (1991, ANOVA for unbalanced data), once making use of the 'lme4' package. The primary objective of this package is to perform a variance component analysis (VCA) according to CLSI EP05-A3 guideline "Evaluation of Precision of Quantitative Measurement Procedures" (2014). There are plotting methods for visualization of an experimental design, plotting random effects and residuals. For ANOVA type estimation two methods for computing ANOVA mean squares are implemented (SWEEP and quadratic forms). The covariance matrix of variance components can be derived, which is used in estimating confidence intervals. Linear hypotheses of fixed effects and LS means can be computed. LS means can be computed at specific values of covariables and with custom weighting schemes for factor variables. See ?VCA for a more comprehensive description of the features.

Maintained by Andre Schuetzenmeister. Last updated 1 years ago.

fortran openblas

17.8 match 2 stars 4.51 score 5 dependents

bioc

TFBSTools:Software Package for Transcription Factor Binding Site (TFBS) Analysis

TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software.

Maintained by Ge Tan. Last updated 4 days ago.

motifannotation generegulation motifdiscovery transcription alignment

6.1 match 28 stars 12.36 score 1.1k scripts 18 dependents

blasbenito

distantia:Advanced Toolset for Efficient Time Series Dissimilarity Analysis

Fast C++ implementation of Dynamic Time Warping for time series dissimilarity analysis, with applications in environmental monitoring and sensor data analysis, climate science, signal processing and pattern recognition, and financial data analysis. Built upon the ideas presented in Benito and Birks (2020) <doi:10.1111/ecog.04895>, provides tools for analyzing time series of varying lengths and structures, including irregular multivariate time series. Key features include individual variable contribution analysis, restricted permutation tests for statistical significance, and imputation of missing data via GAMs. Additionally, the package provides an ample set of tools to prepare and manage time series data.

Maintained by Blas M. Benito. Last updated 25 days ago.

12.8 match 23 stars 5.76 score 11 scripts

usa-npn

rnpn:Interface to the National 'Phenology' Network 'API'

Programmatic interface to the Web Service methods provided by the National 'Phenology' Network (<https://usanpn.org/>), which includes data on various life history events that occur at specific times.

Maintained by Jeff Switzer. Last updated 5 days ago.

data national-phenology-network phenology species web-api

8.1 match 21 stars 8.82 score 109 scripts

pecanproject

PEcAn.assim.batch:PEcAn Functions Used for Ecological Forecasts and Reanalysis

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.

Maintained by Istem Fer. Last updated 2 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants jags cpp

7.0 match 216 stars 9.94 score 20 scripts 2 dependents

emmanuelparadis

ape:Analyses of Phylogenetics and Evolution

Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.

Maintained by Emmanuel Paradis. Last updated 15 hours ago.

openblas cpp

4.0 match 64 stars 17.22 score 13k scripts 599 dependents

bioc

RiboDiPA:Differential pattern analysis for Ribo-seq data

This package performs differential pattern analysis for Ribo-seq data. It identifies genes with significantly different patterns in the ribosome footprint between two conditions. RiboDiPA contains five major components including bam file processing, P-site mapping, data binning, differential pattern analysis and footprint visualization.

Maintained by Ji-Ping Wang. Last updated 3 months ago.

riboseq geneexpression generegulation differentialexpression sequencing coverage alignment rnaseq immunooncology qualitycontrol dataimport software normalization cpp

16.2 match 4.30 score 1 scripts

topepo

caret:Classification and Regression Training

Misc functions for training and plotting classification and regression models.

Maintained by Max Kuhn. Last updated 3 months ago.

3.6 match 1.6k stars 19.24 score 61k scripts 303 dependents

pecanproject

PEcAn.DB:PEcAn Functions Used for Ecological Forecasts and Reanalysis

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.

Maintained by David LeBauer. Last updated 2 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants

5.7 match 216 stars 11.88 score 127 scripts 27 dependents

sollano

forestmangr:Forest Mensuration and Management

Processing forest inventory data with methods such as simple random sampling, stratified random sampling and systematic sampling. There are also functions for yield and growth predictions and model fitting, linear and nonlinear grouped data fitting, and statistical tests. References: Kershaw Jr., Ducey, Beers and Husch (2016). <doi:10.1002/9781118902028>.

Maintained by Sollano Rabelo Braga. Last updated 4 months ago.

8.5 match 17 stars 7.97 score 378 scripts

arutools

ARUtools:Management and Processing of Autonomous Recording Unit (ARU) Data

Parse Autonomous Recording Unit (ARU) data and for sub-sampling recordings. Extract Metadata from your recordings, select a subset of recordings for interpretation, and prepare files for processing on the 'WildTrax' <https://wildtrax.ca/> platform. Read and process metadata from recordings collected using the SongMeter and BAR-LT types of ARUs.

Maintained by David Hope. Last updated 4 months ago.

10.7 match 6.30 score 26 scripts

daijiang

phyr:Model Based Phylogenetic Analysis

A collection of functions to do model-based phylogenetic analysis. It includes functions to calculate community phylogenetic diversity, to estimate correlations among functional traits while accounting for phylogenetic relationships, and to fit phylogenetic generalized linear mixed models. The Bayesian phylogenetic generalized linear mixed models are fitted with the 'INLA' package (<https://www.r-inla.org>).

Maintained by Daijiang Li. Last updated 1 years ago.

bayesian glmm inla phylogeny species-distribution-modeling openblas cpp

7.8 match 31 stars 8.67 score 107 scripts 2 dependents

bioc

isobar:Analysis and quantitation of isobarically tagged MSMS proteomics data

isobar provides methods for preprocessing, normalization, and report generation for the analysis of quantitative mass spectrometry proteomics data labeled with isobaric tags, such as iTRAQ and TMT. Features modules for integrating and validating PTM-centric datasets (isobar-PTM). More information on http://www.ms-isobar.org.

Maintained by Florian P Breitwieser. Last updated 5 months ago.

immunooncology proteomics massspectrometry bioinformatics multiplecomparisons qualitycontrol

9.6 match 10 stars 6.96 score 19 scripts

stuart-lab

Signac:Analysis of Single-Cell Chromatin Data

A framework for the analysis and exploration of single-cell chromatin data. The 'Signac' package contains functions for quantifying single-cell chromatin data, computing per-cell quality control metrics, dimension reduction and normalization, visualization, and DNA sequence motif analysis. Reference: Stuart et al. (2021) <doi:10.1038/s41592-021-01282-5>.

Maintained by Tim Stuart. Last updated 7 months ago.

atac bioinformatics single-cell zlib cpp

5.5 match 349 stars 12.19 score 3.7k scripts 1 dependents

kwb-r

aquanes.report:Automated Reporting Tool for Water Suppliers

Collects, aggregates and visualises operational and analytical data from water suppliers (including a standardised reporting document).

Maintained by Michael Rustler. Last updated 6 years ago.

automated-reporting data-aggregation data-export data-import data-visualisation pilot-plant project-aquanes shiny-app

16.6 match 4.01 score 23 scripts

kwb-r

kwb.pilot:Importing, Aggregating and Visualising Data From KWB Pilot Plants

Collects, aggregates and visualises operational and analytical data from water suppliers (including a standardised reporting document).

Maintained by Michael Rustler. Last updated 2 years ago.

data-aggregation data-import data-visualisation project-aquanes project-mbr40 project-suleman project-ultimate

16.6 match 1 stars 4.01 score 17 scripts

rekyt

funrar:Functional Rarity Indices Computation

Computes functional rarity indices as proposed by Violle et al. (2017) <doi:10.1016/j.tree.2017.02.002>. Various indices can be computed using both regional and local information. Functional Rarity combines both the functional aspect of rarity as well as the extent aspect of rarity. 'funrar' is presented in Grenié et al. (2017) <doi:10.1111/ddi.12629>.

Maintained by Matthias Grenié. Last updated 11 months ago.

ecological-models ecology rarity traits

8.5 match 17 stars 7.85 score 233 scripts 1 dependents

statgenlmu

coala:A Framework for Coalescent Simulation

Coalescent simulators can rapidly simulate biological sequences evolving according to a given model of evolution. You can use this package to specify such models, to conduct the simulations and to calculate additional statistics from the results (Staab, Metzler, 2016 <doi:10.1093/bioinformatics/btw098>). It relies on existing simulators for doing the simulation, and currently supports the programs 'ms', 'msms' and 'scrm'. It also supports finite-sites mutation models by combining the simulators with the program 'seq-gen'. Coala provides functions for calculating certain summary statistics, which can also be applied to actual biological data. One possibility to import data is through the 'PopGenome' package (<https://github.com/pievos101/PopGenome>).

Maintained by Dirk Metzler. Last updated 1 years ago.

coalescent dna evolution popgen simulation cpp

9.4 match 23 stars 7.06 score 84 scripts

spatstat

spatstat.data:Datasets for 'spatstat' Family

Contains all the datasets for the 'spatstat' family of packages.

Maintained by Adrian Baddeley. Last updated 19 hours ago.

kernel-density point-process spatial-analysis spatial-data spatial-data-analysis spatstat statistical-analysis statistical-methods statistical-tests statistics

6.0 match 6 stars 11.00 score 186 scripts 228 dependents

bioc

MSstatsPTM:Statistical Characterization of Post-translational Modifications

MSstatsPTM provides general statistical methods for quantitative characterization of post-translational modifications (PTMs). Supports DDA, DIA, SRM, and tandem mass tag (TMT) labeling. Typically, the analysis involves the quantification of PTM sites (i.e., modified residues) and their corresponding proteins, as well as the integration of the quantification results. MSstatsPTM provides functions for summarization, estimation of PTM site abundance, and detection of changes in PTMs across experimental conditions.

Maintained by Devon Kohler. Last updated 4 months ago.

immunooncology massspectrometry proteomics software differentialexpression onechannel twochannel normalization qualitycontrol post-translational-modification cpp

8.2 match 10 stars 7.98 score 36 scripts 2 dependents

fitzlab-al

gdm:Generalized Dissimilarity Modeling

A toolkit with functions to fit, plot, summarize, and apply Generalized Dissimilarity Models. Mokany K, Ware C, Woolley SNC, Ferrier S, Fitzpatrick MC (2022) <doi:10.1111/geb.13459> Ferrier S, Manion G, Elith J, Richardson K (2007) <doi:10.1111/j.1472-4642.2007.00341.x>.

Maintained by Matt Fitzpatrick. Last updated 2 months ago.

cpp

8.0 match 35 stars 8.12 score 145 scripts

kwb-r

kwb.site:R Package for Scraping Our Offical KWB Website (Before Re-Design in 2021)

This package contains functions for scraping our official [KWB website](https://kompetenz-wasser.de). The data for all projects and people can be collected in order to provide an overview of the website`s content and in order to be integrate that data into a KWB knowledge repo.

Maintained by Michael Rustler. Last updated 3 years ago.

knowledge-repo project-fakin r-selenium rvest web-scraping website

37.5 match 1.70 score 2 scripts

elipousson

legistarapi:Access the Legistar Web API

Access public data using the Legistar Web API.

Maintained by Eli Pousson. Last updated 6 months ago.

legistar

25.7 match 2.48 score 3 scripts

bioc

ribosomeProfilingQC:Ribosome Profiling Quality Control

Ribo-Seq (also named ribosome profiling or footprinting) measures translatome (unlike RNA-Seq, which sequences the transcriptome) by direct quantification of the ribosome-protected fragments (RPFs). This package provides the tools for quality assessment of ribosome profiling. In addition, it can preprocess Ribo-Seq data for subsequent differential analysis.

Maintained by Jianhong Ou. Last updated 1 months ago.

riboseq sequencing generegulation qualitycontrol visualization coverage

13.0 match 4.88 score 17 scripts

isakro

shoredate:Shoreline Dating Coastal Stone Age Sites

Provides tools for shoreline dating coastal Stone Age sites. The implemented method was developed in Roalkvam (2023) <doi:10.1016/j.quascirev.2022.107880> for the Norwegian Skagerrak coast. Although it can be extended to other areas, this also forms the core area for application of the package. Shoreline dating is based on the present-day elevation of a site, a reconstruction of past relative sea-level change, and empirically derived estimates of the likely elevation of the sites above the contemporaneous sea-level when they were in use. The geographical and temporal coverage of the method thus follows from the availability of local geological reconstructions of shoreline displacement and the degree to which the settlements to be dated have been located on or close to the shoreline when they were in use. Methods for numerical treatment and visualisation of the dates are provided, along with basic tools for visualising and evaluating the location of sites.

Maintained by Isak Roalkvam. Last updated 1 years ago.

archaeology relative-sea-level-change shoreline-dating south-eastern-norway

13.0 match 5 stars 4.81 score 13 scripts

cran

sorcering:Soil Organic Carbon and CN Ratio Driven Nitrogen Modelling Framework

Can be used to model the fate of soil organic carbon and soil organic nitrogen and to calculate N mineralisation rates. Provides a framework that numerically solves differential equations of soil organic carbon models based on first-order kinetics and extends these models to include the nitrogen component. The name 'sorcering' is an acronym for 'Soil ORganic Carbon & CN Ratio drIven Nitrogen modellinG framework'.

Maintained by Marc Scherstjanoi. Last updated 5 months ago.

openblas cpp

27.0 match 2.30 score

ropensci

ckanr:Client for the Comprehensive Knowledge Archive Network ('CKAN') API

Client for 'CKAN' API (<https://ckan.org/>). Includes interface to 'CKAN' 'APIs' for search, list, show for packages, organizations, and resources. In addition, provides an interface to the 'datastore' API.

Maintained by Francisco Alves. Last updated 2 years ago.

database open-data ckan api data dataset api-wrapper ckan-api

7.1 match 100 stars 8.67 score 448 scripts 4 dependents

bioc

drawProteins:Package to Draw Protein Schematics from Uniprot API output

This package draws protein schematics from Uniprot API output. From the JSON returned by the GET command, it creates a dataframe from the Uniprot Features API. This dataframe can then be used by geoms based on ggplot2 and base R to draw protein schematics.

Maintained by Paul Brennan. Last updated 5 months ago.

visualization functionalprediction proteomics

7.0 match 34 stars 8.75 score 61 scripts 1 dependents

vivianstats

MAAPER:Analysis of Alternative Polyadenylation Using 3' End-Linked Reads

A computational method developed for model-based analysis of alternative polyadenylation (APA) using 3' end-linked reads. It accurately assigns 3' RNA-seq reads to polyA sites through statistical modeling, and generates multiple statistics for APA analysis. Please also see Li WV, Zheng D, Wang R, Tian B (2021) <doi:10.1186/s13059-021-02429-5>.

Maintained by Wei Vivian Li. Last updated 4 years ago.

alternative-polyadenylation bioinformatics-tool rna-seq

13.0 match 9 stars 4.65 score 7 scripts

ropensci

dendroNetwork:Create Networks of Dendrochronological Series using Pairwise Similarity

Creating dendrochronological networks based on the similarity between tree-ring series or chronologies. The package includes various functions to compare tree-ring curves building upon the 'dplR' package. The networks can be used to visualise and understand the relations between tree-ring curves. These networks are also very useful to estimate the provenance of wood as described in Visser (2021) <DOI:10.5334/jcaa.79> or wood-use within a structure/context/site as described in Visser and Vorst (2022) <DOI:10.1163/27723194-bja10014>.

Maintained by Ronald Visser. Last updated 1 months ago.

visualization graphandnetwork thirdpartyclient network archaeology dendrochronology dendroprovenance network-analysis tree-rings

9.9 match 7 stars 6.05 score 9 scripts

bioc

CAGEfightR:Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

CAGE is a widely used high throughput assay for measuring transcription start site (TSS) activity. CAGEfightR is an R/Bioconductor package for performing a wide range of common data analysis tasks for CAGE and 5'-end data in general. Core functionality includes: import of CAGE TSSs (CTSSs), tag (or unidirectional) clustering for TSS identification, bidirectional clustering for enhancer identification, annotation with transcript and gene models, correlation of TSS and enhancer expression, calculation of TSS shapes, quantification of CAGE expression as expression matrices and genome brower visualization.

Maintained by Malte Thodberg. Last updated 5 months ago.

software transcription coverage geneexpression generegulation peakdetection dataimport datarepresentation transcriptomics sequencing annotation genomebrowsers normalization preprocessing visualization

8.0 match 8 stars 7.46 score 67 scripts 1 dependents

tmcd82070

Rdistance:Distance-Sampling Analyses for Density and Abundance Estimation

Distance-sampling analyses (<doi:10.1007/978-3-319-19219-2>) estimate density and abundance of survey targets (e.g., animals) when detection declines with distance. Distance-sampling is popular ecology, especially when survey targets are observed from aerial platforms (e.g., airplane or drone), surface vessels (e.g., boat or truck), or along walking transects. Both point and line transects can be analyzed. Outputs include overall (study area) density and abundance, effective sampling distances, and model fit statistics. A large suite of classical, parametric detection functions (e.g., half-normal, hazard rate) is included along with uncommon parametric functions (e.g., Gamma, negative exponential). Non-parametric smoothed distance functions are included. Measurement unit integrity is enforced via internal unit conversion. The help files and vignettes have been vetted by multiple authors and tested in workshop settings.

Maintained by Trent McDonald. Last updated 3 days ago.

8.8 match 8 stars 6.51 score 40 scripts

gaynorr

AlphaSimR:Breeding Program Simulations

The successor to the 'AlphaSim' software for breeding program simulation [Faux et al. (2016) <doi:10.3835/plantgenome2016.02.0013>]. Used for stochastic simulations of breeding programs to the level of DNA sequence for every individual. Contained is a wide range of functions for modeling common tasks in a breeding program, such as selection and crossing. These functions allow for constructing simulations of highly complex plant and animal breeding programs via scripting in the R software environment. Such simulations can be used to evaluate overall breeding program performance and conduct research into breeding program design, such as implementation of genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS') for fast simulation of biallelic sequences according to a population demographic history [Chen et al. (2009) <doi:10.1101/gr.083634.108>].

Maintained by Chris Gaynor. Last updated 5 months ago.

breeding genomics simulation openblas cpp openmp

5.6 match 47 stars 10.22 score 534 scripts 2 dependents

tbep-tech

tbeptools:Data and Indicators for the Tampa Bay Estuary Program

Several functions are provided for working with Tampa Bay Estuary Program data and indicators, including the water quality report card, tidal creek assessments, Tampa Bay Nekton Index, Tampa Bay Benthic Index, seagrass transect data, habitat report card, and fecal indicator bacteria. Additional functions are provided for miscellaneous tasks, such as reference library curation.

Maintained by Marcus Beck. Last updated 9 days ago.

data-analysis tampa-bay tbep water-quality

7.3 match 10 stars 7.86 score 133 scripts

cran

betapart:Partitioning Beta Diversity into Turnover and Nestedness Components

Functions to compute pair-wise dissimilarities (distance matrices) and multiple-site dissimilarities, separating the turnover and nestedness-resultant components of taxonomic (incidence and abundance based), functional and phylogenetic beta diversity.

Maintained by Andres Baselga. Last updated 2 years ago.

13.9 match 2 stars 3.97 score 6 dependents

noaa-ocm

SWMPrExtension:Functions for Analyzing and Plotting Estuary Monitoring Data

Tools for performing routine analysis and plotting tasks with environmental data from the System Wide Monitoring Program of the National Estuarine Research Reserve System <https://cdmo.baruch.sc.edu/>. This package builds on the functionality of the 'SWMPr' package <https://cran.r-project.org/package=SWMPr>, which is used to retrieve and organize the data. The combined set of tools address common challenges associated with continuous time series data for environmental decision making, and are intended for use in annual reporting activities. References: Beck, Marcus W. (2016) <ISSN 2073-4859><https://journal.r-project.org/archive/2016-1/beck.pdf> Rudis, Bob (2014) <https://rud.is/b/2014/11/16/moving-the-earth-well-alaska-hawaii-with-r/>. United States Environmental Protection Agency (2015) <https://cfpub.epa.gov/si/si_public_record_Report.cfm?Lab=OWOW&dirEntryId=327030>. United States Environmental Protection Agency (2012) <https://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.646.1973&rep=rep1&type=pdf>.

Maintained by Matt Dornback. Last updated 2 years ago.

10.7 match 12 stars 5.10 score 42 scripts

bioc

DiffBind:Differential Binding Analysis of ChIP-Seq Peak Data

Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.

Maintained by Rory Stark. Last updated 2 months ago.

sequencing chipseq atacseq dnaseseq methylseq ripseq differentialpeakcalling differentialmethylation generegulation histonemodification peakdetection biomedicalinformatics cellbiology multiplecomparison normalization reportwriting epigenetics functionalgenomics curl bzip2 xz-utils zlib cpp

7.6 match 7.13 score 512 scripts 2 dependents

talgalili

installr:Using R to Install Stuff on Windows OS (Such As: R, 'Rtools', 'RStudio', 'Git', and More!)

R is great for installing software. Through the 'installr' package you can automate the updating of R (on Windows, using updateR()) and install new software. Software installation is initiated through a GUI (just run installr()), or through functions such as: install.Rtools(), install.pandoc(), install.git(), and many more. The updateR() command performs the following: finding the latest R version, downloading it, running the installer, deleting the installation file, copy and updating old packages to the new R installation.

Maintained by Tal Galili. Last updated 1 years ago.

5.3 match 273 stars 10.19 score 1.2k scripts

hristotomov

PolyTrend:Trend Classification Algorithm

This algorithm classifies the trends into linear, quadratic, cubic, concealed and no-trend types. The "concealed trends" are those trends that possess quadratic or cubic forms, but the net change from the start of the time period to the end of the time period hasn't been significant. The "no-trend" category includes simple linear trends with statistically in-significant slope coefficient.

Maintained by Hristo Tomov. Last updated 9 years ago.

49.5 match 1.08 score 12 scripts

project-gen3sis

gen3sis:General Engine for Eco-Evolutionary Simulations

Contains an engine for spatially-explicit eco-evolutionary mechanistic models with a modular implementation and several support functions. It allows exploring the consequences of ecological and macroevolutionary processes across realistic or theoretical spatio-temporal landscapes on biodiversity patterns as a general term. Reference: Oskar Hagen, Benjamin Flueck, Fabian Fopp, Juliano S. Cabral, Florian Hartig, Mikael Pontarp, Thiago F. Rangel, Loic Pellissier (2021) "gen3sis: A general engine for eco-evolutionary simulations of the processes that shape Earth's biodiversity" <doi:10.1371/journal.pbio.3001340>.

Maintained by Oskar Hagen. Last updated 1 years ago.

biodiversity ecology evolution mechanistic model modeling simulation cpp

7.1 match 29 stars 7.56 score 69 scripts

cran

zetadiv:Functions to Compute Compositional Turnover Using Zeta Diversity

Functions to compute compositional turnover using zeta-diversity, the number of species shared by multiple assemblages. The package includes functions to compute zeta-diversity for a specific number of assemblages and to compute zeta-diversity for a range of numbers of assemblages. It also includes functions to explain how zeta-diversity varies with distance and with differences in environmental variables between assemblages, using generalised linear models, linear models with negative constraints, generalised additive models,shape constrained additive models, and I-splines.

Maintained by Guillaume Latombe. Last updated 3 years ago.

18.5 match 3 stars 2.89 score 64 scripts

dmurdoch

rgl:3D Visualization Using OpenGL

Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.

Maintained by Duncan Murdoch. Last updated 2 months ago.

graphics opengl rgl webgl libglu libglvnd libpng libx11 freetype cpp

3.0 match 91 stars 17.49 score 7.3k scripts 300 dependents

zhaokg

Rbeast:Bayesian Change-Point Detection and Time Series Decomposition

Interpretation of time series data is affected by model choices. Different models can give different or even contradicting estimates of patterns, trends, and mechanisms for the same data--a limitation alleviated by the Bayesian estimator of abrupt change,seasonality, and trend (BEAST) of this package. BEAST seeks to improve time series decomposition by forgoing the "single-best-model" concept and embracing all competing models into the inference via a Bayesian model averaging scheme. It is a flexible tool to uncover abrupt changes (i.e., change-points), cyclic variations (e.g., seasonality), and nonlinear trends in time-series observations. BEAST not just tells when changes occur but also quantifies how likely the detected changes are true. It detects not just piecewise linear trends but also arbitrary nonlinear trends. BEAST is applicable to real-valued time series data of all kinds, be it for remote sensing, economics, climate sciences, ecology, and hydrology. Example applications include its use to identify regime shifts in ecological data, map forest disturbance and land degradation from satellite imagery, detect market trends in economic data, pinpoint anomaly and extreme events in climate data, and unravel system dynamics in biological data. Details on BEAST are reported in Zhao et al. (2019) <doi:10.1016/j.rse.2019.04.034>.

Maintained by Kaiguang Zhao. Last updated 6 months ago.

anomoly-detection bayesian-time-series breakpoint-detection changepoint-detection interrupted-time-series seasonality-analysis structural-breakpoint technical-analysis time-series time-series-decomposition trend trend-analysis

6.9 match 302 stars 7.63 score 89 scripts

friendly

heplots:Visualizing Hypothesis Tests in Multivariate Linear Models

Provides HE plot and other functions for visualizing hypothesis tests in multivariate linear models. HE plots represent sums-of-squares-and-products matrices for linear hypotheses and for error using ellipses (in two dimensions) and ellipsoids (in three dimensions). The related 'candisc' package provides visualizations in a reduced-rank canonical discriminant space when there are more than a few response variables.

Maintained by Michael Friendly. Last updated 9 days ago.

linear-hypotheses matrices multivariate-linear-models plot repeated-measure-designs visualizing-hypothesis-tests

4.5 match 9 stars 11.49 score 1.1k scripts 7 dependents

bioc

borealis:Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution

Borealis is an R library performing outlier analysis for count-based bisulfite sequencing data. It detectes outlier methylated CpG sites from bisulfite sequencing (BS-seq). The core of Borealis is modeling Beta-Binomial distributions. This can be useful for rare disease diagnoses.

Maintained by Garrett Jenkinson. Last updated 5 months ago.

sequencing coverage dnamethylation differentialmethylation

13.7 match 3.73 score 27 scripts

mages

ChainLadder:Statistical Methods and Models for Claims Reserving in General Insurance

Various statistical methods and models which are typically used for the estimation of outstanding claims reserves in general insurance, including those to estimate the claims development result as required under Solvency II.

Maintained by Markus Gesmann. Last updated 1 months ago.

5.1 match 82 stars 10.04 score 196 scripts 2 dependents

bioc

rtracklayer:R interface to genome annotation files and the UCSC genome browser

Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.

Maintained by Michael Lawrence. Last updated 8 days ago.

annotation visualization dataimport zlib openssl curl

4.0 match 12.66 score 6.7k scripts 481 dependents

d-carlson

archdata:Example Datasets from Archaeological Research

The archdata package provides several types of data that are typically used in archaeological research. It provides all of the data sets used in "Quantitative Methods in Archaeology Using R" by David L Carlson, one of the Cambridge Manuals in Archaeology.

Maintained by David L. Carlson. Last updated 4 years ago.

14.4 match 1 stars 3.50 score 138 scripts

admahood

neonPlantEcology:Process NEON Plant Data for Ecological Analysis

Downloading and organizing plant presence and percent cover data from the National Ecological Observatory Network <https://www.neonscience.org>.

Maintained by Adam Mahood. Last updated 2 months ago.

9.9 match 8 stars 5.08 score 7 scripts

ncordon

imbalance:Preprocessing Algorithms for Imbalanced Datasets

Class imbalance usually damages the performance of classifiers. Thus, it is important to treat data before applying a classifier algorithm. This package includes recent resampling algorithms in the literature: (Barua et al. 2014) <doi:10.1109/tkde.2012.232>; (Das et al. 2015) <doi:10.1109/tkde.2014.2324567>, (Zhang et al. 2014) <doi:10.1016/j.inffus.2013.12.003>; (Gao et al. 2014) <doi:10.1016/j.neucom.2014.02.006>; (Almogahed et al. 2014) <doi:10.1007/s00500-014-1484-5>. It also includes an useful interface to perform oversampling.

Maintained by Ignacio Cordón. Last updated 5 years ago.

binary-classification imbalanced-data oversampling openblas cpp

7.0 match 36 stars 7.14 score 98 scripts

bioc

SingleMoleculeFootprinting:Analysis tools for Single Molecule Footprinting (SMF) data

SingleMoleculeFootprinting provides functions to analyze Single Molecule Footprinting (SMF) data. Following the workflow exemplified in its vignette, the user will be able to perform basic data analysis of SMF data with minimal coding effort. Starting from an aligned bam file, we show how to perform quality controls over sequencing libraries, extract methylation information at the single molecule level accounting for the two possible kind of SMF experiments (single enzyme or double enzyme), classify single molecules based on their patterns of molecular occupancy, plot SMF information at a given genomic location.

Maintained by Guido Barzaghi. Last updated 28 days ago.

dnamethylation coverage nucleosomepositioning datarepresentation epigenetics methylseq qualitycontrol sequencing

7.7 match 2 stars 6.43 score 27 scripts

biodiverse

unmarked:Models for Data from Unmarked Animals

Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates. References: Kellner et al. (2023) <doi:10.1111/2041-210X.14123>, Fiske and Chandler (2011) <doi:10.18637/jss.v043.i10>.

Maintained by Ken Kellner. Last updated 1 days ago.

openblas cpp openmp

3.8 match 4 stars 13.03 score 652 scripts 12 dependents

fmestre1

MetaLandSim:Landscape and Range Expansion Simulation

Tools to generate random landscape graphs, evaluate species occurrence in dynamic landscapes, simulate future landscape occupation and evaluate range expansion when new empty patches are available (e.g. as a result of climate change). References: Mestre, F., Canovas, F., Pita, R., Mira, A., Beja, P. (2016) <doi:10.1016/j.envsoft.2016.03.007>; Mestre, F., Risk, B., Mira, A., Beja, P., Pita, R. (2017) <doi:10.1016/j.ecolmodel.2017.06.013>; Mestre, F., Pita, R., Mira, A., Beja, P. (2020) <doi:10.1186/s12898-019-0273-5>.

Maintained by Frederico Mestre. Last updated 2 years ago.

biogeography ecology metapopulation species

9.7 match 3 stars 5.10 score 28 scripts

pecanproject

PEcAn.data.land:PEcAn Functions Used for Ecological Forecasts and Reanalysis

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.

Maintained by Mike Dietze. Last updated 2 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants jags cpp

5.2 match 216 stars 9.32 score 19 scripts 10 dependents

sujit-sahu

bmstdr:Bayesian Modeling of Spatio-Temporal Data with R

Fits, validates and compares a number of Bayesian models for spatial and space time point referenced and areal unit data. Model fitting is done using several packages: 'rstan', 'INLA', 'spBayes', 'spTimer', 'spTDyn', 'CARBayes' and 'CARBayesST'. Model comparison is performed using the DIC and WAIC, and K-fold cross-validation where the user is free to select their own subset of data rows for validation. Sahu (2022) <doi:10.1201/9780429318443> describes the methods in detail.

Maintained by Sujit K. Sahu. Last updated 1 years ago.

bayesian modelling spatio-temporal-data cpp

9.8 match 15 stars 4.95 score 12 scripts

bioc

rnaEditr:Statistical analysis of RNA editing sites and hyper-editing regions

RNAeditr analyzes site-specific RNA editing events, as well as hyper-editing regions. The editing frequencies can be tested against binary, continuous or survival outcomes. Multiple covariate variables as well as interaction effects can also be incorporated in the statistical models.

Maintained by Lanyu Zhang. Last updated 5 months ago.

genetarget epigenetics dimensionreduction featureextraction regression survival rnaseq

10.8 match 3 stars 4.48 score 9 scripts

daijiang

hillR:Diversity Through Hill Numbers

Calculate taxonomic, functional and phylogenetic diversity measures through Hill Numbers proposed by Chao, Chiu and Jost (2014) <doi:10.1146/annurev-ecolsys-120213-091540>.

Maintained by Daijiang Li. Last updated 11 months ago.

biodiversity hill-numbers

5.9 match 33 stars 8.21 score 157 scripts 3 dependents

bioc

hiReadsProcessor:Functions to process LM-PCR reads from 454/Illumina data

hiReadsProcessor contains set of functions which allow users to process LM-PCR products sequenced using any platform. Given an excel/txt file containing parameters for demultiplexing and sample metadata, the functions automate trimming of adaptors and identification of the genomic product. Genomic products are further processed for QC and abundance quantification.

Maintained by Nirav V Malani. Last updated 5 months ago.

sequencing preprocessing

11.5 match 4.18 score 7 scripts

bioc

rifi:'rifi' analyses data from rifampicin time series created by microarray or RNAseq

'rifi' analyses data from rifampicin time series created by microarray or RNAseq. 'rifi' is a transcriptome data analysis tool for the holistic identification of transcription and decay associated processes. The decay constants and the delay of the onset of decay is fitted for each probe/bin. Subsequently, probes/bins of equal properties are combined into segments by dynamic programming, independent of a existing genome annotation. This allows to detect transcript segments of different stability or transcriptional events within one annotated gene. In addition to the classic decay constant/half-life analysis, 'rifi' detects processing sites, transcription pausing sites, internal transcription start sites in operons, sites of partial transcription termination in operons, identifies areas of likely transcriptional interference by the collision mechanism and gives an estimate of the transcription velocity. All data are integrated to give an estimate of continous transcriptional units, i.e. operons. Comprehensive output tables and visualizations of the full genome result and the individual fits for all probes/bins are produced.

Maintained by Jens Georg. Last updated 5 months ago.

rnaseq differentialexpression generegulation transcriptomics regression microarray software

10.3 match 4.60 score 1 scripts

mrc-ide

eppasm:Age-structured EPP Model for HIV Epidemic Estimates

What the package does (one paragraph).

Maintained by Jeff Eaton. Last updated 3 months ago.

9.4 match 6 stars 5.04 score 34 scripts 3 dependents

cran

SPSL:Site Percolation on Square Lattices (SPSL)

Provides basic functionality for labeling iso- & anisotropic percolation clusters on 2D & 3D square lattices with various lattice sizes, occupation probabilities, von Neumann & Moore (1,d)-neighborhoods, and random variables weighting the percolation lattice sites.

Maintained by Pavel V. Moskalev. Last updated 6 years ago.

32.0 match 1.48 score 1 dependents

doi-usgs

toxEval:Exploring Biological Relevance of Environmental Chemistry Observations

Data analysis package for estimating potential biological effects from chemical concentrations in environmental samples. Included are a set of functions to analyze, visualize, and organize measured concentration data as it relates to user-selected chemical-biological interaction benchmark data such as water quality criteria. The intent of these analyses is to develop a better understanding of the potential biological relevance of environmental chemistry data. Results can be used to prioritize which chemicals at which sites may be of greatest concern. These methods are meant to be used as a screening technique to predict potential for biological influence from chemicals that ultimately need to be validated with direct biological assays. A description of the analysis can be found in Blackwell (2017) <doi:10.1021/acs.est.7b01613>.

Maintained by Laura DeCicco. Last updated 3 months ago.

toxicity water-quality

6.3 match 21 stars 7.34 score 58 scripts

pecanproject

PEcAn.ED2:PEcAn Package for Integration of ED2 Model

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation. This package provides functions to link the Ecosystem Demography Model, version 2, to PEcAn.

Maintained by Mike Dietze. Last updated 2 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants jags cpp

5.3 match 216 stars 8.72 score 145 scripts

elipousson

sharepointr:Read and Write from SharePoint Sites

A R package extending Microsoft365R to make it easier to read, write, and work with SharePoint items, lists, and plans.

Maintained by Eli Pousson. Last updated 5 months ago.

microsoft-365 sharepoint-online

11.3 match 25 stars 4.04 score 11 scripts

inlabru-org

inlabru:Bayesian Latent Gaussian Modelling using INLA and Extensions

Facilitates spatial and general latent Gaussian modeling using integrated nested Laplace approximation via the INLA package (<https://www.r-inla.org>). Additionally, extends the GAM-like model class to more general nonlinear predictor expressions, and implements a log Gaussian Cox process likelihood for modeling univariate and spatial point processes based on ecological survey data. Model components are specified with general inputs and mapping methods to the latent variables, and the predictors are specified via general R expressions, with separate expressions for each observation likelihood model in multi-likelihood models. A prediction method based on fast Monte Carlo sampling allows posterior prediction of general expressions of the latent variables. Ecology-focused introduction in Bachl, Lindgren, Borchers, and Illian (2019) <doi:10.1111/2041-210X.13168>.

Maintained by Finn Lindgren. Last updated 4 days ago.

3.6 match 96 stars 12.62 score 832 scripts 6 dependents

emmanuelparadis

pegas:Population and Evolutionary Genetics Analysis System

Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and network, and median-joining networks.

Maintained by Emmanuel Paradis. Last updated 1 years ago.

6.0 match 7.53 score 576 scripts 18 dependents

bioc

ASEB:Predict Acetylated Lysine Sites

ASEB is an R package to predict lysine sites that can be acetylated by a specific KAT-family.

Maintained by Likun Wang. Last updated 5 months ago.

proteomics cpp

10.6 match 4.20 score 1 scripts

lter

lterdatasampler:Educational Dataset Examples from the Long Term Ecological Research Program

Curated datasets from US Long Term Ecological Research sites.

Maintained by Allison Horst. Last updated 1 years ago.

data-science ecology lter-science

7.1 match 50 stars 6.26 score 240 scripts

ediorg

ecocomDP:Tools to Create, Use, and Convert ecocomDP Data

Work with the Ecological Community Data Design Pattern. 'ecocomDP' is a flexible data model for harmonizing ecological community surveys, in a research question agnostic format, from source data published across repositories, and with methods that keep the derived data up-to-date as the underlying sources change. Described in O'Brien et al. (2021), <doi:10.1016/j.ecoinf.2021.101374>.

Maintained by Colin Smith. Last updated 7 months ago.

5.4 match 32 stars 8.22 score 77 scripts

bioc

msgbsR:msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions

Pipeline for the anaysis of a MS-GBS experiment.

Maintained by Benjamin Mayne. Last updated 5 months ago.

immunooncology differentialmethylation dataimport epigenetics methylseq

9.8 match 4.48 score 1 scripts

ohdsi

EvidenceSynthesis:Synthesizing Causal Evidence in a Distributed Research Network

Routines for combining causal effect estimates and study diagnostics across multiple data sites in a distributed study, without sharing patient-level data. Allows for normal and non-normal approximations of the data-site likelihood of the effect parameter.

Maintained by Martijn Schuemie. Last updated 6 months ago.

hades openjdk

7.4 match 8 stars 5.87 score 31 scripts

bioc

APAlyzer:A toolkit for APA analysis using RNA-seq data

Perform 3'UTR APA, Intronic APA and gene expression analysis using RNA-seq data.

Maintained by Ruijia Wang. Last updated 5 months ago.

sequencing rnaseq differentialexpression geneexpression generegulation annotation dataimport software ative-polyadenylation bioinformatics-tool rna-seq

7.5 match 8 stars 5.81 score 9 scripts

biorgeo

bioregion:Comparison of Bioregionalisation Methods

The main purpose of this package is to propose a transparent methodological framework to compare bioregionalisation methods based on hierarchical and non-hierarchical clustering algorithms (Kreft & Jetz (2010) <doi:10.1111/j.1365-2699.2010.02375.x>) and network algorithms (Lenormand et al. (2019) <doi:10.1002/ece3.4718> and Leroy et al. (2019) <doi:10.1111/jbi.13674>).

Maintained by Maxime Lenormand. Last updated 11 days ago.

biogeography bioregion bioregionalization cpp

6.9 match 7 stars 6.27 score 11 scripts

dnychka

fields:Tools for Spatial Data

For curve, surface and function fitting with an emphasis on splines, spatial data, geostatistics, and spatial statistics. The major methods include cubic, and thin plate splines, Kriging, and compactly supported covariance functions for large data sets. The splines and Kriging methods are supported by functions that can determine the smoothing parameter (nugget and sill variance) and other covariance function parameters by cross validation and also by restricted maximum likelihood. For Kriging there is an easy to use function that also estimates the correlation scale (range parameter). A major feature is that any covariance function implemented in R and following a simple format can be used for spatial prediction. There are also many useful functions for plotting and working with spatial data as images. This package also contains an implementation of sparse matrix methods for large spatial data sets and currently requires the sparse matrix (spam) package. Use help(fields) to get started and for an overview. The fields source code is deliberately commented and provides useful explanations of numerical details as a companion to the manual pages. The commented source code can be viewed by expanding the source code version and looking in the R subdirectory. The reference for fields can be generated by the citation function in R and has DOI <doi:10.5065/D6W957CT>. Development of this package was supported in part by the National Science Foundation Grant 1417857, the National Center for Atmospheric Research, and Colorado School of Mines. See the Fields URL for a vignette on using this package and some background on spatial statistics.

Maintained by Douglas Nychka. Last updated 9 months ago.

fortran

3.4 match 15 stars 12.60 score 7.7k scripts 295 dependents

mikejohnson51

climateR:climateR

Find, subset, and retrive geospatial data by AOI.

Maintained by Mike Johnson. Last updated 3 months ago.

aoi climate dataset geospatial gridded-climate-data weather

4.9 match 187 stars 8.74 score 156 scripts 1 dependents

ghislainv

hSDM:Hierarchical Bayesian Species Distribution Models

User-friendly and fast set of functions for estimating parameters of hierarchical Bayesian species distribution models (Latimer and others 2006 <doi:10.1890/04-0609>). Such models allow interpreting the observations (occurrence and abundance of a species) as a result of several hierarchical processes including ecological processes (habitat suitability, spatial dependence and anthropogenic disturbance) and observation processes (species detectability). Hierarchical species distribution models are essential for accurately characterizing the environmental response of species, predicting their probability of occurrence, and assessing uncertainty in the model results.

Maintained by Ghislain Vieilledent. Last updated 2 years ago.

gsl

7.1 match 9 stars 6.04 score 41 scripts

bioc

crisprDesign:Comprehensive design of CRISPR gRNAs for nucleases and base editors

Provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences. This includes on- and off-target search, on-target efficiency scoring, off-target scoring, full gene and TSS contextual annotations, and SNP annotation (human only). It currently support five types of CRISPR modalities (modes of perturbations): CRISPR knockout, CRISPR activation, CRISPR inhibition, CRISPR base editing, and CRISPR knockdown. All types of CRISPR nucleases are supported, including DNA- and RNA-target nucleases such as Cas9, Cas12a, and Cas13d. All types of base editors are also supported. gRNA design can be performed on reference genomes, transcriptomes, and custom DNA and RNA sequences. Both unpaired and paired gRNA designs are enabled.

Maintained by Jean-Philippe Fortin. Last updated 11 days ago.

crispr functionalgenomics genetarget bioconductor bioconductor-package crispr-cas9 crispr-design crispr-target genomics-analysis grna grna-sequence grna-sequences sgrna sgrna-design

5.2 match 22 stars 8.28 score 80 scripts 3 dependents

dvrbts

labdsv:Ordination and Multivariate Analysis for Ecology

A variety of ordination and community analyses useful in analysis of data sets in community ecology. Includes many of the common ordination methods, with graphical routines to facilitate their interpretation, as well as several novel analyses.

Maintained by David W. Roberts. Last updated 2 years ago.

fortran

7.0 match 3 stars 6.08 score 452 scripts 13 dependents

discindo

newscatcheR:Programmatically Collect Normalized News from (Almost) Any Website

Programmatically collect normalized news from (almost) any website. An 'R' clone of the <https://github.com/kotartemiy/newscatcher> 'Python' module.

Maintained by Novica Nakov. Last updated 1 years ago.

hacktoberfest news-sites newscatcher rss-feed tidyrss

7.5 match 30 stars 5.65 score 7 scripts

agqhammond

UKFE:UK Flood Estimation

Functions to implement the methods of the Flood Estimation Handbook (FEH), associated updates and the revitalised flood hydrograph model (ReFH). Currently the package uses NRFA peak flow dataset version 13. Aside from FEH functionality, further hydrological functions are available. Most of the methods implemented in this package are described in one or more of the following: "Flood Estimation Handbook", Centre for Ecology & Hydrology (1999, ISBN:0 948540 94 X). "Flood Estimation Handbook Supplementary Report No. 1", Kjeldsen (2007, ISBN:0 903741 15 7). "Regional Frequency Analysis - an approach based on L-moments", Hosking & Wallis (1997, ISBN: 978 0 521 01940 8). "Proposal of the extreme rank plot for extreme value analysis: with an emphasis on flood frequency studies", Hammond (2019, <doi:10.2166/nh.2019.157>). "Making better use of local data in flood frequency estimation", Environment Agency (2017, ISBN: 978 1 84911 387 8). "Sampling uncertainty of UK design flood estimation" , Hammond (2021, <doi:10.2166/nh.2021.059>). "Improving the FEH statistical procedures for flood frequency estimation", Environment Agency (2008, ISBN: 978 1 84432 920 5). "Low flow estimation in the United Kingdom", Institute of Hydrology (1992, ISBN 0 948540 45 1). Wallingford HydroSolutions, (2016, <http://software.hydrosolutions.co.uk/winfap4/Urban-Adjustment-Procedure-Technical-Note.pdf>). Data from the UK National River Flow Archive (<https://nrfa.ceh.ac.uk/>, terms and conditions: <https://nrfa.ceh.ac.uk/costs-terms-and-conditions>).

Maintained by Anthony Hammond. Last updated 1 months ago.

23.5 match 1 stars 1.78 score

bioc

ChIPComp:Quantitative comparison of multiple ChIP-seq datasets

ChIPComp detects differentially bound sharp binding sites across multiple conditions considering matching control.

Maintained by Li Chen. Last updated 5 months ago.

chipseq sequencing transcription genetics coverage multiplecomparison dataimport

9.1 match 4.49 score 51 scripts

bioc

scanMiR:scanMiR

A set of tools for working with miRNA affinity models (KdModels), efficiently scanning for miRNA binding sites, and predicting target repression. It supports scanning using miRNA seeds, full miRNA sequences (enabling 3' alignment) and KdModels, and includes the prediction of slicing and TDMD sites. Finally, it includes utility and plotting functions (e.g. for the visual representation of miRNA-target alignment).

Maintained by Pierre-Luc Germain. Last updated 5 months ago.

mirna sequencematching alignment

6.9 match 5.89 score 52 scripts 1 dependents

tntp

tntpr:Data Analysis Tools Customized for TNTP

An assortment of functions and templates customized to meet the needs of data analysts at the non-profit organization TNTP. Includes functions for branded colors and plots, credentials management, repository set-up, and other common analytic tasks.

Maintained by Dustin Pashouwer. Last updated 4 months ago.

6.9 match 7 stars 5.83 score 13 scripts

aurelienroyer

SEAHORS:Spatial Exploration of ArcHaeological Objects in R Shiny

An R 'Shiny' application dedicated to the intra-site spatial analysis of piece-plotted archaeological remains, making the two and three-dimensional spatial exploration of archaeological data as user-friendly as possible. Documentation about 'SEAHORS' is provided by the vignette included in this package and by the companion scientific paper: Royer, Discamps, Plutniak, Thomas (2023, PCI Archaeology, <doi:10.5281/zenodo.7674698>).

Maintained by Sebastien Plutniak. Last updated 1 years ago.

archaeology spatial-visualizations

8.6 match 5 stars 4.70 score 4 scripts

lter

ltertools:Tools Developed by the Long Term Ecological Research Community

Set of the data science tools created by various members of the Long Term Ecological Research (LTER) community. These functions were initially written largely as standalone operations and have later been aggregated into this package.

Maintained by Nicholas Lyon. Last updated 23 days ago.

data-science lter-science

8.1 match 3 stars 4.95 score 4 scripts

bioc

TAPseq:Targeted scRNA-seq primer design for TAP-seq

Design primers for targeted single-cell RNA-seq used by TAP-seq. Create sequence templates for target gene panels and design gene-specific primers using Primer3. Potential off-targets can be estimated with BLAST. Requires working installations of Primer3 and BLASTn.

Maintained by Andreas R. Gschwind. Last updated 5 months ago.

singlecell sequencing technology crispr pooledscreens

7.4 match 4 stars 5.38 score 9 scripts

bioc

motifbreakR:A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites

We introduce motifbreakR, which allows the biologist to judge in the first place whether the sequence surrounding the polymorphism is a good match, and in the second place how much information is gained or lost in one allele of the polymorphism relative to another. MotifbreakR is both flexible and extensible over previous offerings; giving a choice of algorithms for interrogation of genomes with motifs from public sources that users can choose from; these are 1) a weighted-sum probability matrix, 2) log-probabilities, and 3) weighted by relative entropy. MotifbreakR can predict effects for novel or previously described variants in public databases, making it suitable for tasks beyond the scope of its original design. Lastly, it can be used to interrogate any genome curated within Bioconductor (currently there are 32 species, a total of 109 versions).

Maintained by Simon Gert Coetzee. Last updated 5 months ago.

chipseq visualization motifannotation transcription

4.4 match 28 stars 8.96 score 103 scripts

adeverse

adespatial:Multivariate Multiscale Spatial Analysis

Tools for the multiscale spatial analysis of multivariate data. Several methods are based on the use of a spatial weighting matrix and its eigenvector decomposition (Moran's Eigenvectors Maps, MEM). Several approaches are described in the review Dray et al (2012) <doi:10.1890/11-1183.1>.

Maintained by Aurélie Siberchicot. Last updated 13 days ago.

openblas

3.5 match 36 stars 11.06 score 398 scripts 2 dependents

bioc

GUIDEseq:GUIDE-seq and PEtag-seq analysis pipeline

The package implements GUIDE-seq and PEtag-seq analysis workflow including functions for filtering UMI and reads with low coverage, obtaining unique insertion sites (proxy of cleavage sites), estimating the locations of the insertion sites, aka, peaks, merging estimated insertion sites from plus and minus strand, and performing off target search of the extended regions around insertion sites with mismatches and indels.

Maintained by Lihua Julie Zhu. Last updated 5 months ago.

immunooncology generegulation sequencing workflowstep crispr

8.8 match 4.45 score 14 scripts

pet221

SSNbler:Assemble 'SSN' Objects

Import, create and assemble data needed to fit spatial-statistical stream-network models using the 'SSN2' package for 'R'. Streams, observations, and prediction locations are represented as simple features and specific tools provided to define topological relationships between features; calculate the hydrologic distances (with flow-direction preserved) and the spatial additive function used to weight converging stream segments; and export the topological, spatial, and attribute information to an `SSN` (spatial stream network) object, which can be efficiently stored, accessed and analysed in 'R'. A detailed description of methods used to calculate and format the spatial data can be found in Peterson, E.E. and Ver Hoef, J.M., (2014) <doi:10.18637/jss.v056.i02>.

Maintained by Erin Peterson. Last updated 6 months ago.

6.5 match 10 stars 6.01 score 17 scripts

hristotomov

DBEST:Detecting Breakpoints and Estimating Segments in Trend

A program for analyzing vegetation time series, with two algorithms: 1) change detection algorithm that detects trend changes, determines their type (abrupt or non-abrupt), and estimates their timing, magnitude, number, and direction; 2) generalization algorithm that simplifies the temporal trend into main features. The user can set the number of major breakpoints or magnitude of greatest changes of interest for detection, and can control the generalization process by setting an additional parameter of generalization-percentage.

Maintained by Hristo Tomov. Last updated 7 years ago.

18.0 match 5 stars 2.18 score 10 scripts

roelandkindt

BiodiversityR:Package for Community Ecology and Suitability Analysis

Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.

Maintained by Roeland Kindt. Last updated 2 months ago.

5.3 match 16 stars 7.42 score 390 scripts 2 dependents

wagner-s

MultIS:Reconstruction of Clones from Integration Site Readouts and Visualization

Tools necessary to reconstruct clonal affiliations from temporally and/or spatially separated measurements of viral integration sites. For this means it utilizes correlations present in the relative readouts of the integration sites. Furthermore, facilities for filtering of the data and visualization of different steps in the pipeline are provided with the package.

Maintained by Sebastian Wagner. Last updated 4 years ago.

19.5 match 2.00 score 1 scripts

kenaho1

asbio:A Collection of Statistical Tools for Biologists

Contains functions from: Aho, K. (2014) Foundational and Applied Statistics for Biologists using R. CRC/Taylor and Francis, Boca Raton, FL, ISBN: 978-1-4398-7338-0.

Maintained by Ken Aho. Last updated 2 months ago.

5.3 match 5 stars 7.32 score 310 scripts 3 dependents

txm676

sars:Fit and Compare Species-Area Relationship Models Using Multimodel Inference

Implements the basic elements of the multi-model inference paradigm for up to twenty species-area relationship models (SAR), using simple R list-objects and functions, as in Triantis et al. 2012 <DOI:10.1111/j.1365-2699.2011.02652.x>. The package is scalable and users can easily create their own model and data objects. Additional SAR related functions are provided.

Maintained by Thomas J. Matthews. Last updated 11 days ago.

5.8 match 9 stars 6.67 score 95 scripts

long39ng

remmy:API Client for 'Lemmy'

An HTTP API client for 'Lemmy' (<https://github.com/LemmyNet/lemmy>) in R. Code and documentation are generated from the official 'JavaScript' client source (<https://github.com/LemmyNet/lemmy-js-client>).

Maintained by Long Nguyen. Last updated 2 years ago.

lemmy

14.3 match 2.70 score 4 scripts

earthyscience

REddyProc:Post Processing of (Half-)Hourly Eddy-Covariance Measurements

Standard and extensible Eddy-Covariance data post-processing (Wutzler et al. (2018) <doi:10.5194/bg-15-5015-2018>) includes uStar-filtering, gap-filling, and flux-partitioning. The Eddy-Covariance (EC) micrometeorological technique quantifies continuous exchange fluxes of gases, energy, and momentum between an ecosystem and the atmosphere. It is important for understanding ecosystem dynamics and upscaling exchange fluxes. (Aubinet et al. (2012) <doi:10.1007/978-94-007-2351-1>). This package inputs pre-processed (half-)hourly data and supports further processing. First, a quality-check and filtering is performed based on the relationship between measured flux and friction velocity (uStar) to discard biased data (Papale et al. (2006) <doi:10.5194/bg-3-571-2006>). Second, gaps in the data are filled based on information from environmental conditions (Reichstein et al. (2005) <doi:10.1111/j.1365-2486.2005.001002.x>). Third, the net flux of carbon dioxide is partitioned into its gross fluxes in and out of the ecosystem by night-time based and day-time based approaches (Lasslop et al. (2010) <doi:10.1111/j.1365-2486.2009.02041.x>).

Maintained by Thomas Wutzler. Last updated 4 months ago.

cpp

3.4 match 63 stars 11.22 score 163 scripts 16 dependents

jgregoriods

spDates:Analysis of Spatial Gradients in Radiocarbon Dates

Inspired by space-time regressions often performed to assess the expansion of the Neolithic from the Near East to Europe (Pinhasi et al. 2005 <doi:10.1371/journal.pbio.0030410>). Test for significant correlations between the (earliest) radiocarbon dates of archaeological sites and their respective distances from a hypothetical center of origin. Both ordinary least squares (OLS) and reduced major axis (RMA) methods are supported (Russell et al. 2014 <doi:10.1371/journal.pone.0087854>). It is also possible to iterate over many sites to identify the most likely origin.

Maintained by Jonas Gregorio de Souza. Last updated 2 years ago.

radiocarbon-dates

14.2 match 1 stars 2.70 score 2 scripts

bioc

CAGEr:Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

The _CAGEr_ package identifies transcription start sites (TSS) and their usage frequency from CAGE (Cap Analysis Gene Expression) sequencing data. It normalises raw CAGE tag count, clusters TSSs into tag clusters (TC) and aggregates them across multiple CAGE experiments to construct consensus clusters (CC) representing the promoterome. CAGEr provides functions to profile expression levels of these clusters by cumulative expression and rarefaction analysis, and outputs the plots in ggplot2 format for further facetting and customisation. After clustering, CAGEr performs analyses of promoter width and detects differential usage of TSSs (promoter shifting) between samples. CAGEr also exports its data as genome browser tracks, and as R objects for downsteam expression analysis by other Bioconductor packages such as DESeq2, CAGEfightR, or seqArchR.

Maintained by Charles Plessy. Last updated 5 months ago.

preprocessing sequencing normalization functionalgenomics transcription geneexpression clustering visualization

6.2 match 6.12 score 73 scripts

bioc

BiSeq:Processing and analyzing bisulfite sequencing data

The BiSeq package provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data. In particular, it implements an algorithm to detect differentially methylated regions (DMRs). The package takes already aligned BS data from one or multiple samples.

Maintained by Katja Hebestreit. Last updated 5 months ago.

genetics sequencing methylseq dnamethylation

8.0 match 4.78 score 30 scripts

ecor

RMAWGEN:Multi-Site Auto-Regressive Weather GENerator

S3 and S4 functions are implemented for spatial multi-site stochastic generation of daily time series of temperature and precipitation. These tools make use of Vector AutoRegressive models (VARs). The weather generator model is then saved as an object and is calibrated by daily instrumental "Gaussianized" time series through the 'vars' package tools. Once obtained this model, it can it can be used for weather generations and be adapted to work with several climatic monthly time series.

Maintained by Emanuele Cordano. Last updated 26 days ago.

6.8 match 3 stars 5.62 score 115 scripts 4 dependents

ddalthorp

dwp:Density-Weighted Proportion

Fit a Poisson regression to carcass distance data and integrate over the searched area at a wind farm to estimate the fraction of carcasses falling in the searched area and format the output for use as the dwp parameter in the 'GenEst' or 'eoa' package for estimating bird and bat mortality, following Dalthorp, et al. (2022) <arXiv:2201.10064>.

Maintained by Daniel Dalthorp. Last updated 2 years ago.

14.1 match 1 stars 2.70 score

jcoliver

lifeR:Identify Sites for Your Bird List

A suite of tools to use the 'eBird' database (<https://ebird.org/home/>) and APIs to compare users' species lists to recent observations and create a report of the top sites to visit to see new species.

Maintained by Jeffrey Oliver. Last updated 1 months ago.

7.9 match 4 stars 4.78 score 6 scripts

vusaverse

vvtableau:R Interface for 'Tableau' Services

Provides an R interface for interacting with the 'Tableau' Server. It allows users to perform various operations such as publishing workbooks, refreshing data extracts, and managing users using the 'Tableau' REST API (see <https://help.tableau.com/current/api/rest_api/en-us/REST/rest_api_ref.htm> for details). Additionally, it includes functions to perform manipulations on local 'Tableau' workbooks.

Maintained by Tomer Iwan. Last updated 7 months ago.

rest-api tableau tableau-dashboards tableau-desktop tableau-rest-api tableau-server

6.0 match 7 stars 6.25 score 16 scripts

massbays-tech

MassWateR:Quality Control and Analysis of Massachusetts Water Quality Data

Methods for quality control and exploratory analysis of surface water quality data collected in Massachusetts, USA. Functions are developed to facilitate data formatting for the Water Quality Exchange Network <https://www.epa.gov/waterdata/water-quality-data-upload-wqx> and reporting of data quality objectives to state agencies. Quality control methods are from Massachusetts Department of Environmental Protection (2020) <https://www.mass.gov/orgs/massachusetts-department-of-environmental-protection>.

Maintained by Marcus Beck. Last updated 10 days ago.

7.1 match 13 stars 5.26 score 10 scripts

bioc

icetea:Integrating Cap Enrichment with Transcript Expression Analysis

icetea (Integrating Cap Enrichment with Transcript Expression Analysis) provides functions for end-to-end analysis of multiple 5'-profiling methods such as CAGE, RAMPAGE and MAPCap, beginning from raw reads to detection of transcription start sites using replicates. It also allows performing differential TSS detection between group of samples, therefore, integrating the mRNA cap enrichment information with transcript expression analysis.

Maintained by Vivek Bhardwaj. Last updated 5 months ago.

immunooncology transcription geneexpression sequencing rnaseq transcriptomics differentialexpression cage expression rna-seq

7.3 match 2 stars 5.08 score 7 scripts

trotsiuk

r3PG:Simulating Forest Growth using the 3-PG Model

Provides a flexible and easy-to-use interface for the Physiological Processes Predicting Growth (3-PG) model written in Fortran. The r3PG serves as a flexible and easy-to-use interface for the 3-PGpjs (monospecific, evenaged and evergreen forests) described in Landsberg & Waring (1997) <doi:10.1016/S0378-1127(97)00026-1> and the 3-PGmix (deciduous, uneven-aged or mixed-species forests) described in Forrester & Tang (2016) <doi:10.1016/j.ecolmodel.2015.07.010>.

Maintained by Volodymyr Trotsiuk. Last updated 10 months ago.

fortran glibc

6.4 match 27 stars 5.83 score 25 scripts

wjbraun

DAAG:Data Analysis and Graphics Data and Functions

Functions and data sets used in examples and exercises in the text Maindonald, J.H. and Braun, W.J. (2003, 2007, 2010) "Data Analysis and Graphics Using R", and in an upcoming Maindonald, Braun, and Andrews text that builds on this earlier text.

Maintained by W. John Braun. Last updated 11 months ago.

4.5 match 8.25 score 1.2k scripts 1 dependents

zhangrenl

geneHapR:Gene Haplotype Statistics, Phenotype Association and Visualization

Import genome variants data and perform gene haplotype Statistics, visualization and phenotype association with 'R'.

Maintained by Zhang Renliang. Last updated 6 months ago.

nucleosomepositioning dataimport

7.3 match 13 stars 5.11 score 8 scripts

cran

MASS:Support Functions and Datasets for Venables and Ripley's MASS

Functions and datasets to support Venables and Ripley, "Modern Applied Statistics with S" (4th edition, 2002).

Maintained by Brian Ripley. Last updated 16 days ago.

3.5 match 19 stars 10.53 score 11k dependents

birdlifeinternational

track2KBA:Identifying Important Areas from Animal Tracking Data

Functions for preparing and analyzing animal tracking data, with the intention of identifying areas which are potentially important at the population level and therefore of conservation interest. Areas identified using this package may be checked against global or regionally-defined criteria, such as those set by the Key Biodiversity Area program. The method published herein is described in full in Beal et al. 2021 <doi:10.1111/2041-210X.13713>.

Maintained by Martin Beal. Last updated 9 months ago.

5.5 match 11 stars 6.51 score 59 scripts

bioboot

bio3d:Biological Structure Analysis

Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information.

Maintained by Barry Grant. Last updated 5 months ago.

zlib cpp

4.3 match 5 stars 8.49 score 1.4k scripts 10 dependents

bioc

artMS:Analytical R tools for Mass Spectrometry

artMS provides a set of tools for the analysis of proteomics label-free datasets. It takes as input the MaxQuant search result output (evidence.txt file) and performs quality control, relative quantification using MSstats, downstream analysis and integration. artMS also provides a set of functions to re-format and make it compatible with other analytical tools, including, SAINTq, SAINTexpress, Phosfate, and PHOTON. Check [http://artms.org](http://artms.org) for details.

Maintained by David Jimenez-Morales. Last updated 5 months ago.

proteomics differentialexpression biomedicalinformatics systemsbiology massspectrometry annotation qualitycontrol genesetenrichment clustering normalization immunooncology multiplecomparison analysis analytical ap-ms bioconductor bioinformatics mass-spectrometry phosphoproteomics post-translational-modification quantitative-analysis

5.6 match 14 stars 6.41 score 13 scripts

pecanproject

PEcAnAssimSequential:PEcAn Functions Used for Ecological Forecasts and Reanalysis

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.

Maintained by Mike Dietze. Last updated 2 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants jags cpp

4.4 match 216 stars 8.11 score 35 scripts

bioc

ChIPanalyser:ChIPanalyser: Predicting Transcription Factor Binding Sites

ChIPanalyser is a package to predict and understand TF binding by utilizing a statistical thermodynamic model. The model incorporates 4 main factors thought to drive TF binding: Chromatin State, Binding energy, Number of bound molecules and a scaling factor modulating TF binding affinity. Taken together, ChIPanalyser produces ChIP-like profiles that closely mimic the patterns seens in real ChIP-seq data.

Maintained by Patrick C.N. Martin. Last updated 5 months ago.

software biologicalquestion workflowstep transcription sequencing chiponchip coverage alignment chipseq sequencematching dataimport peakdetection

8.2 match 4.38 score 12 scripts

eco-hydro

phenofit:Extract Remote Sensing Vegetation Phenology

The merits of 'TIMESAT' and 'phenopix' are adopted. Besides, a simple and growing season dividing method and a practical snow elimination method based on Whittaker were proposed. 7 curve fitting methods and 4 phenology extraction methods were provided. Parameters boundary are considered for every curve fitting methods according to their ecological meaning. And 'optimx' is used to select best optimization method for different curve fitting methods. Reference: Kong, D., (2020). R package: A state-of-the-art Vegetation Phenology extraction package, phenofit version 0.3.1, <doi:10.5281/zenodo.5150204>; Kong, D., Zhang, Y., Wang, D., Chen, J., & Gu, X. (2020). Photoperiod Explains the Asynchronization Between Vegetation Carbon Phenology and Vegetation Greenness Phenology. Journal of Geophysical Research: Biogeosciences, 125(8), e2020JG005636. <doi:10.1029/2020JG005636>; Kong, D., Zhang, Y., Gu, X., & Wang, D. (2019). A robust method for reconstructing global MODIS EVI time series on the Google Earth Engine. ISPRS Journal of Photogrammetry and Remote Sensing, 155, 13–24; Zhang, Q., Kong, D., Shi, P., Singh, V.P., Sun, P., 2018. Vegetation phenology on the Qinghai-Tibetan Plateau and its response to climate change (1982–2013). Agric. For. Meteorol. 248, 408–417. <doi:10.1016/j.agrformet.2017.10.026>.

Maintained by Dongdong Kong. Last updated 1 months ago.

phenology remote-sensing openblas cpp openmp

4.6 match 78 stars 7.71 score 332 scripts

giopogg

jtdm:Joint Modelling of Functional Traits

Fitting and analyzing a Joint Trait Distribution Model. The Joint Trait Distribution Model is implemented in the Bayesian framework using conjugate priors and posteriors, thus guaranteeing fast inference. In particular the package computes joint probabilities and multivariate confidence intervals, and enables the investigation of how they depend on the environment through partial response curves. The method implemented by the package is described in Poggiato et al. (2023) <doi:10.1111/geb.13706>.

Maintained by Giovanni Poggiato. Last updated 6 months ago.

7.2 match 9 stars 4.95 score 7 scripts

neonscience

neonUtilities:Utilities for Working with NEON Data

NEON data packages can be accessed through the NEON Data Portal <https://www.neonscience.org> or through the NEON Data API (see <https://data.neonscience.org/data-api> for documentation). Data delivered from the Data Portal are provided as monthly zip files packaged within a parent zip file, while individual files can be accessed from the API. This package provides tools that aid in discovering, downloading, and reformatting data prior to use in analyses. This includes downloading data via the API, merging data tables by type, and converting formats. For more information, see the readme file at <https://github.com/NEONScience/NEON-utilities>.

Maintained by Claire Lunch. Last updated 1 months ago.

3.3 match 57 stars 10.66 score 944 scripts 15 dependents

apear9

rdwplus:Inverse Distance Weighted Percent Land Use for Streams

Compute spatially explicit land-use metrics for stream survey sites in GRASS GIS and R as an open-source implementation of IDW-PLUS (Inverse Distance Weighted Percent Land Use for Streams). The package includes functions for preprocessing digital elevation and streams data, and one function to compute all the spatially explicit land use metrics described in Peterson et al. (2011) <doi:10.1111/j.1365-2427.2010.02507.x> and previously implemented by Peterson and Pearse (2017) <doi:10.1111/1752-1688.12558> in ArcGIS-Python as IDW-PLUS.

Maintained by Alan Pearse. Last updated 1 months ago.

9.1 match 4 stars 3.90 score 6 scripts

phiala

ecodist:Dissimilarity-Based Functions for Ecological Analysis

Dissimilarity-based analysis functions including ordination and Mantel test functions, intended for use with spatial and community ecological data. The original package description is in Goslee and Urban (2007) <doi:10.18637/jss.v022.i07>, with further statistical detail in Goslee (2010) <doi:10.1007/s11258-009-9641-0>.

Maintained by Sarah Goslee. Last updated 1 years ago.

openblas

3.6 match 9 stars 9.84 score 566 scripts 9 dependents

btorobrob

cesr:Trend analysis of Constant Effort Site ringing data

Functions for reading EuroCES data in Euring format to produce annual indices of abundance, productivity and survival. Designed to primarily analyse data from schemes with 10-12 visits per year following methods used by the BTO. Use read.ces() to read in data, extract.data() and index() to do abundance/productivity trends and extract.ch() and mark.ces() to estimate survival probabilities.

Maintained by Rob Robinson. Last updated 1 years ago.

cpp

16.3 match 1 stars 2.16 score 29 scripts

matt-s-gibbs

SWTools:Helper Tools for Australian Hydrologists

Functions to speed up work flow for hydrological analysis. Focused on Australian climate data (SILO climate data), hydrological models (eWater Source) and in particular South Australia (<https://water.data.sa.gov.au> hydrological data).

Maintained by Matt Gibbs. Last updated 5 months ago.

8.8 match 5 stars 4.00 score 3 scripts

vegandevs

vegan:Community Ecology Package

Ordination methods, diversity analysis and other functions for community and vegetation ecologists.

Maintained by Jari Oksanen. Last updated 16 days ago.

ecological-modelling ecology ordination fortran openblas

1.8 match 472 stars 19.41 score 15k scripts 440 dependents

bluegreen-labs

phenocamr:Facilitates 'PhenoCam' Data Access and Time Series Post-Processing

Programmatic interface to the 'PhenoCam' web services (<https://phenocam.nau.edu/webcam>). Allows for easy downloading of 'PhenoCam' data directly to your R workspace or your computer and provides post-processing routines for consistent and easy timeseries outlier detection, smoothing and estimation of phenological transition dates. Methods for this package are described in detail in Hufkens et. al (2018) <doi:10.1111/2041-210X.12970>.

Maintained by Koen Hufkens. Last updated 1 years ago.

phenocam phenocam-data phenology-modelling remote-sensing

5.2 match 22 stars 6.69 score 75 scripts 1 dependents

cgoo4

usedthese:Summarises Package & Function Usage

Consistent with 'knitr' syntax highlighting, 'usedthese' adds a summary table of package & function usage to a Quarto document and enables aggregation of usage across a website.

Maintained by Carl Goodwin. Last updated 8 months ago.

quarto

5.1 match 7 stars 6.70 score 120 scripts

bioc

ModCon:Modifying splice site usage by changing the mRNP code, while maintaining the genetic code

Collection of functions to calculate a nucleotide sequence surrounding for splice donors sites to either activate or repress donor usage. The proposed alternative nucleotide sequence encodes the same amino acid and could be applied e.g. in reporter systems to silence or activate cryptic splice donor sites.

Maintained by Johannes Ptok. Last updated 5 months ago.

functionalgenomics alternativesplicing

8.6 match 1 stars 4.00 score 2 scripts

remkoduursma

smatr:(Standardised) Major Axis Estimation and Testing Routines

Methods for fitting bivariate lines in allometry using the major axis (MA) or standardised major axis (SMA), and for making inferences about such lines. The available methods of inference include confidence intervals and one-sample tests for slope and elevation, testing for a common slope or elevation amongst several allometric lines, constructing a confidence interval for a common slope or elevation, and testing for no shift along a common axis, amongst several samples. See Warton et al. 2012 <doi:10.1111/j.2041-210X.2011.00153.x> for methods description.

Maintained by Remko Duursma. Last updated 7 years ago.

6.6 match 1 stars 5.20 score 212 scripts 5 dependents

wraff

wrMisc:Analyze Experimental High-Throughput (Omics) Data

The efficient treatment and convenient analysis of experimental high-throughput (omics) data gets facilitated through this collection of diverse functions. Several functions address advanced object-conversions, like manipulating lists of lists or lists of arrays, reorganizing lists to arrays or into separate vectors, merging of multiple entries, etc. Another set of functions provides speed-optimized calculation of standard deviation (sd), coefficient of variance (CV) or standard error of the mean (SEM) for data in matrixes or means per line with respect to additional grouping (eg n groups of replicates). A group of functions facilitate dealing with non-redundant information, by indexing unique, adding counters to redundant or eliminating lines with respect redundancy in a given reference-column, etc. Help is provided to identify very closely matching numeric values to generate (partial) distance matrixes for very big data in a memory efficient manner or to reduce the complexity of large data-sets by combining very close values. Other functions help aligning a matrix or data.frame to a reference using partial matching or to mine an experimental setup to extract patterns of replicate samples. Many times large experimental datasets need some additional filtering, adequate functions are provided. Convenient data normalization is supported in various different modes, parameter estimation via permutations or boot-strap as well as flexible testing of multiple pair-wise combinations using the framework of 'limma' is provided, too. Batch reading (or writing) of sets of files and combining data to arrays is supported, too.

Maintained by Wolfgang Raffelsberger. Last updated 7 months ago.

7.7 match 4.44 score 33 scripts 4 dependents

r-lib

ymlthis:Write 'YAML' for 'R Markdown', 'bookdown', 'blogdown', and More

Write 'YAML' front matter for R Markdown and related documents. Work with 'YAML' objects more naturally and write the resulting 'YAML' to your clipboard or to 'YAML' files related to your project.

Maintained by Malcolm Barrett. Last updated 3 years ago.

3.4 match 165 stars 9.91 score 196 scripts 14 dependents

ropensci

cde:Download Data from the Catchment Data Explorer Website

Facilitates searching, download and plotting of Water Framework Directive (WFD) reporting data for all waterbodies within the UK Environment Agency area. The types of data that can be downloaded are: WFD status classification data, Reasons for Not Achieving Good (RNAG) status, objectives set for waterbodies, measures put in place to improve water quality and details of associated protected areas. The site accessed is <https://environment.data.gov.uk/catchment-planning/>. The data are made available under the Open Government Licence v3.0 <https://www.nationalarchives.gov.uk/doc/open-government-licence/version/3/>.

Maintained by Rob Briers. Last updated 5 months ago.

7.5 match 5 stars 4.52 score 22 scripts

bioc

hiAnnotator:Functions for annotating GRanges objects

hiAnnotator contains set of functions which allow users to annotate a GRanges object with custom set of annotations. The basic philosophy of this package is to take two GRanges objects (query & subject) with common set of seqnames (i.e. chromosomes) and return associated annotation per seqnames and rows from the query matching seqnames and rows from the subject (i.e. genes or cpg islands). The package comes with three types of annotation functions which calculates if a position from query is: within a feature, near a feature, or count features in defined window sizes. Moreover, each function is equipped with parallel backend to utilize the foreach package. In addition, the package is equipped with wrapper functions, which finds appropriate columns needed to make a GRanges object from a common data frame.

Maintained by Nirav V Malani. Last updated 5 months ago.

software annotation

7.1 match 4.65 score 15 scripts 1 dependents

bioc

methylumi:Handle Illumina methylation data

This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.

Maintained by Sean Davis. Last updated 5 months ago.

dnamethylation twochannel preprocessing qualitycontrol cpgisland

3.3 match 9 stars 9.90 score 89 scripts 9 dependents

r-lib

usethis:Automate Package and Project Setup

Automate package and project setup tasks that are otherwise performed manually. This includes setting up unit testing, test coverage, continuous integration, Git, 'GitHub', licenses, 'Rcpp', 'RStudio' projects, and more.

Maintained by Jennifer Bryan. Last updated 11 days ago.

github setup

1.9 match 869 stars 17.54 score 5.6k scripts 336 dependents

ropensci

rnoaa:'NOAA' Weather Data from R

Client for many 'NOAA' data sources including the 'NCDC' climate 'API' at <https://www.ncdc.noaa.gov/cdo-web/webservices/v2>, with functions for each of the 'API' 'endpoints': data, data categories, data sets, data types, locations, location categories, and stations. In addition, we have an interface for 'NOAA' sea ice data, the 'NOAA' severe weather inventory, 'NOAA' Historical Observing 'Metadata' Repository ('HOMR') data, 'NOAA' storm data via 'IBTrACS', tornado data via the 'NOAA' storm prediction center, and more.

Maintained by Daniel Hocking. Last updated 1 months ago.

earth science climate precipitation temperature storm buoy ncdc noaa tornadoe sea ice isd noaa-data

3.4 match 334 stars 9.39 score 788 scripts 4 dependents

bnaras

distcomp:Computations over Distributed Data without Aggregation

Implementing algorithms and fitting models when sites (possibly remote) share computation summaries rather than actual data over HTTP with a master R process (using 'opencpu', for example). A stratified Cox model and a singular value decomposition are provided. The former makes direct use of code from the R 'survival' package. (That is, the underlying Cox model code is derived from that in the R 'survival' package.) Sites may provide data via several means: CSV files, Redcap API, etc. An extensible design allows for new methods to be added in the future and includes facilities for local prototyping and testing. Web applications are provided (via 'shiny') for the implemented methods to help in designing and deploying the computations.

Maintained by Balasubramanian Narasimhan. Last updated 9 months ago.

6.0 match 9 stars 5.33 score 47 scripts

iembry

ie2miscdata:Irucka Embry's Miscellaneous USGS Data Collection

A collection of Irucka Embry's miscellaneous USGS data sets (USGS Parameter codes with fixed values, USGS global time zone codes, and US Air Force Global Engineering Weather Data). Irucka created these data sets while a Cherokee Nation Technology Solutions (CNTS) United States Geological Survey (USGS) Contractor and/or USGS employee.

Maintained by Irucka Embry. Last updated 2 years ago.

8.0 match 4.00 score

ropensci

RSelenium:R Bindings for 'Selenium WebDriver'

Provides a set of R bindings for the 'Selenium 2.0 WebDriver' (see <https://www.selenium.dev/documentation/> for more information) using the 'JsonWireProtocol' (see <https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol> for more information). 'Selenium 2.0 WebDriver' allows driving a web browser natively as a user would either locally or on a remote machine using the Selenium server it marks a leap forward in terms of web browser automation. Selenium automates web browsers (commonly referred to as browsers). Using RSelenium you can automate browsers locally or remotely.

Maintained by Jonathan Völkle. Last updated 2 years ago.

rselenium selenium webdriver

2.4 match 344 stars 13.38 score 1.9k scripts 12 dependents

bzhanglab

WebGestaltR:Gene Set Analysis Toolkit WebGestaltR

The web version WebGestalt <https://www.webgestalt.org> supports 12 organisms, 354 gene identifiers and 321,251 function categories. Users can upload the data and functional categories with their own gene identifiers. In addition to the Over-Representation Analysis, WebGestalt also supports Gene Set Enrichment Analysis and Network Topology Analysis. The user-friendly output report allows interactive and efficient exploration of enrichment results. The WebGestaltR package not only supports all above functions but also can be integrated into other pipeline or simultaneously analyze multiple gene lists.

Maintained by John Elizarraras. Last updated 30 days ago.

rust cargo

3.5 match 35 stars 9.14 score 180 scripts

afrimapr

afrihealthsites:Geographic locations of African health facilities from different sources

African healthsite locations from healthsites.io and WHO/KEMRI-WELLCOME.

Maintained by Andy South. Last updated 4 years ago.

africa african-health-sites

6.7 match 31 stars 4.79 score 40 scripts

bioc

MSstatsLiP:LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

Tools for LiP peptide and protein significance analysis. Provides functions for summarization, estimation of LiP peptide abundance, and detection of changes across conditions. Utilizes functionality across the MSstats family of packages.

Maintained by Devon Kohler. Last updated 5 months ago.

immunooncology massspectrometry proteomics software differentialexpression onechannel twochannel normalization qualitycontrol cpp

5.7 match 7 stars 5.62 score 5 scripts

ropensci

dataspice:Create Lightweight Schema.org Descriptions of Data

The goal of 'dataspice' is to make it easier for researchers to create basic, lightweight, and concise metadata files for their datasets. These basic files can then be used to make useful information available during analysis, create a helpful dataset "README" webpage, and produce more complex metadata formats to aid dataset discovery. Metadata fields are based on the 'Schema.org' and 'Ecological Metadata Language' standards.

Maintained by Bryce Mecum. Last updated 4 years ago.

data dataset metadata schema-org unconf unconf18

4.3 match 162 stars 7.45 score 25 scripts

rstudio

bookdown:Authoring Books and Technical Documents with R Markdown

Output formats and utilities for authoring books and technical documents with R Markdown.

Maintained by Yihui Xie. Last updated 2 days ago.

book bookdown epub gitbook html latex rmarkdown

1.8 match 3.9k stars 17.51 score 1.7k scripts 136 dependents

tbep-tech

tbeploads:Calculate Loading Data to Tampa Bay

Loading data from major sources to Tampa Bay are calculated on a monthly or annual basis. Major sources include domestic point source (reuse, end of pipe), industrial point source, material losses, non-point sources (MS4), atmospheric deposition, and groundwater.

Maintained by Marcus Beck. Last updated 7 months ago.

data-analysis loads tampa-bay tbep tbnmc water-quality

8.3 match 3.81 score 3 scripts

thinkr-open

papillon:Build And Highlight Package Documentation With Customized Templates

Helps creating company visual identity. Build your templates for your package vignettes, reports with {bookdown}, package presentation with {pkgdown}. Highlight your documentation in your projects. Allow for code folding.

Maintained by Sébastien Rochette. Last updated 2 years ago.

7.3 match 11 stars 4.34 score 4 scripts

bioc

esATAC:An Easy-to-use Systematic pipeline for ATACseq data analysis

This package provides a framework and complete preset pipeline for quantification and analysis of ATAC-seq Reads. It covers raw sequencing reads preprocessing (FASTQ files), reads alignment (Rbowtie2), aligned reads file operations (SAM, BAM, and BED files), peak calling (F-seq), genome annotations (Motif, GO, SNP analysis) and quality control report. The package is managed by dataflow graph. It is easy for user to pass variables seamlessly between processes and understand the workflow. Users can process FASTQ files through end-to-end preset pipeline which produces a pretty HTML report for quality control and preliminary statistical results, or customize workflow starting from any intermediate stages with esATAC functions easily and flexibly.

Maintained by Zheng Wei. Last updated 5 months ago.

immunooncology sequencing dnaseq qualitycontrol alignment preprocessing coverage atacseq dnaseseq atac-seq bioconductor pipeline cpp openjdk

5.1 match 23 stars 6.11 score 3 scripts

bodkan

slendr:A Simulation Framework for Spatiotemporal Population Genetics

A framework for simulating spatially explicit genomic data which leverages real cartographic information for programmatic and visual encoding of spatiotemporal population dynamics on real geographic landscapes. Population genetic models are then automatically executed by the 'SLiM' software by Haller et al. (2019) <doi:10.1093/molbev/msy228> behind the scenes, using a custom built-in simulation 'SLiM' script. Additionally, fully abstract spatial models not tied to a specific geographic location are supported, and users can also simulate data from standard, non-spatial, random-mating models. These can be simulated either with the 'SLiM' built-in back-end script, or using an efficient coalescent population genetics simulator 'msprime' by Baumdicker et al. (2022) <doi:10.1093/genetics/iyab229> with a custom-built 'Python' script bundled with the R package. Simulated genomic data is saved in a tree-sequence format and can be loaded, manipulated, and summarised using tree-sequence functionality via an R interface to the 'Python' module 'tskit' by Kelleher et al. (2019) <doi:10.1038/s41588-019-0483-y>. Complete model configuration, simulation and analysis pipelines can be therefore constructed without a need to leave the R environment, eliminating friction between disparate tools for population genetic simulations and data analysis.

Maintained by Martin Petr. Last updated 12 days ago.

popgen population-genetics simulations spatial-statistics

3.4 match 56 stars 9.15 score 88 scripts

obrl-soil

mpspline2:Mass-Preserving Spline Functions for Soil Data

A low-dependency implementation of GSIF::mpspline() <https://r-forge.r-project.org/scm/viewvc.php/pkg/R/mpspline.R?view=markup&revision=240&root=gsif>, which applies a mass-preserving spline to soil attributes. Splining soil data is a safe way to make continuous down-profile estimates of attributes measured over discrete, often discontinuous depth intervals.

Maintained by Lauren OBrien. Last updated 1 years ago.

6.9 match 6 stars 4.50 score 35 scripts

bioc

REDseq:Analysis of high-throughput sequencing data processed by restriction enzyme digestion

The package includes functions to build restriction enzyme cut site (RECS) map, distribute mapped sequences on the map with five different approaches, find enriched/depleted RECSs for a sample, and identify differentially enriched/depleted RECSs between samples.

Maintained by Lihua Julie Zhu. Last updated 5 months ago.

sequencing sequencematching preprocessing

8.9 match 3.48 score 15 scripts

petebaker

cropgrowdays:Crop Growing Degree Days and Agrometeorological Calculations

Calculate agrometeorological variables for crops including growing degree days (McMaster, GS & Wilhelm, WW (1997) <doi:10.1016/S0168-1923(97)00027-0>), cumulative rainfall, number of stress days and cumulative or mean radiation and evaporation. Convert dates to day of year and vice versa. Also, download curated and interpolated Australian weather data from the Queensland Government DES longpaddock website <https://www.longpaddock.qld.gov.au/>. This data is freely available under the Creative Commons 4.0 licence.

Maintained by Peter Baker. Last updated 1 years ago.

7.4 match 4.11 score 13 scripts

bioc

QSutils:Quasispecies Diversity

Set of utility functions for viral quasispecies analysis with NGS data. Most functions are equally useful for metagenomic studies. There are three main types: (1) data manipulation and exploration—functions useful for converting reads to haplotypes and frequencies, repairing reads, intersecting strand haplotypes, and visualizing haplotype alignments. (2) diversity indices—functions to compute diversity and entropy, in which incidence, abundance, and functional indices are considered. (3) data simulation—functions useful for generating random viral quasispecies data.

Maintained by Mercedes Guerrero-Murillo. Last updated 5 months ago.

software genetics dnaseq geneticvariability sequencing alignment sequencematching dataimport

5.5 match 5.56 score 8 scripts 1 dependents

condwanaland

fishdata:A Small Collection of Fish Population Datasets

A collection of four datasets based around the population dynamics of migratory fish. Datasets contain both basic size information on a per fish basis, as well as otolith data that contains a per day record of fish growth history. All data in this package was collected by the author, from 2015-2016, in the Wellington region of New Zealand.

Maintained by Conor Neilson. Last updated 4 years ago.

6.9 match 1 stars 4.45 score 28 scripts

bioc

DECIPHER:Tools for curating, analyzing, and manipulating biological sequences

A toolset for deciphering and managing biological sequences.

Maintained by Erik Wright. Last updated 5 days ago.

clustering genetics sequencing dataimport visualization microarray qualitycontrol qpcr alignment wholegenome microbiome immunooncology geneprediction openmp

3.6 match 8.40 score 1.1k scripts 14 dependents