Showing 200 of total 230 results (show query)
kbroman
qtl:Tools for Analyzing QTL Experiments
Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits. Broman et al. (2003) <doi:10.1093/bioinformatics/btg112>.
Maintained by Karl W Broman. Last updated 7 months ago.
45.5 match 80 stars 12.79 score 2.4k scripts 29 dependents
jfrench
smerc:Statistical Methods for Regional Counts
Implements statistical methods for analyzing the counts of areal data, with a focus on the detection of spatial clusters and clustering. The package has a heavy emphasis on spatial scan methods, which were first introduced by Kulldorff and Nagarwalla (1995) <doi:10.1002/sim.4780140809> and Kulldorff (1997) <doi:10.1080/03610929708831995>.
Maintained by Joshua French. Last updated 5 months ago.
63.8 match 3 stars 6.11 score 45 scripts 3 dependents
jazznbass
scan:Single-Case Data Analyses for Single and Multiple Baseline Designs
A collection of procedures for analysing, visualising, and managing single-case data. These include piecewise linear regression models, multilevel models, overlap indices ('PND', 'PEM', 'PAND', 'PET', 'tau-u', 'baseline corrected tau', 'CDC'), and randomization tests. Data preparation functions support outlier detection, handling missing values, scaling, and custom transformations. An export function helps to generate html, word, and latex tables in a publication friendly style. More details can be found in the online book 'Analyzing single-case data with R and scan', Juergen Wilbert (2025) <https://jazznbass.github.io/scan-Book/>.
Maintained by Juergen Wilbert. Last updated 15 days ago.
59.6 match 4 stars 6.42 score 62 scripts 1 dependents
adokter
bioRad:Biological Analysis and Visualization of Weather Radar Data
Extract, visualize and summarize aerial movements of birds and insects from weather radar data. See Dokter, A. M. et al. (2018) "bioRad: biological analysis and visualization of weather radar data" <doi:10.1111/ecog.04028> for a software paper describing package and methodologies.
Maintained by Adriaan M. Dokter. Last updated 20 days ago.
aeroecologyenrameumetnet-operalifewatchmovement-ecologynexradoscibioradarweather-radarwsr-88d
41.3 match 29 stars 8.65 score 56 scripts
martin3141
spant:MR Spectroscopy Analysis Tools
Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data. The package includes methods for spectral fitting: Wilson (2021) <DOI:10.1002/mrm.28385> and spectral alignment: Wilson (2018) <DOI:10.1002/mrm.27605>.
Maintained by Martin Wilson. Last updated 30 days ago.
brainmrimrsmrshubspectroscopyfortran
25.4 match 25 stars 8.52 score 81 scripts
spatstat
spatstat.explore:Exploratory Data Analysis for the 'spatstat' Family
Functionality for exploratory data analysis and nonparametric analysis of spatial data, mainly spatial point patterns, in the 'spatstat' family of packages. (Excludes analysis of spatial data on a linear network, which is covered by the separate package 'spatstat.linnet'.) Methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.
Maintained by Adrian Baddeley. Last updated 1 months ago.
cluster-detectionconfidence-intervalshypothesis-testingk-functionroc-curvesscan-statisticssignificance-testingsimulation-envelopesspatial-analysisspatial-data-analysisspatial-sharpeningspatial-smoothingspatial-statistics
19.4 match 1 stars 10.17 score 67 scripts 148 dependents
rqtl
qtl2:Quantitative Trait Locus Mapping in Experimental Crosses
Provides a set of tools to perform quantitative trait locus (QTL) analysis in experimental crosses. It is a reimplementation of the 'R/qtl' package to better handle high-dimensional data and complex cross designs. Broman et al. (2019) <doi:10.1534/genetics.118.301595>.
Maintained by Karl W Broman. Last updated 8 days ago.
17.7 match 34 stars 9.48 score 1.1k scripts 5 dependents
bioc
SCAN.UPC:Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
SCAN is a microarray normalization method to facilitate personalized-medicine workflows. Rather than processing microarray samples as groups, which can introduce biases and present logistical challenges, SCAN normalizes each sample individually by modeling and removing probe- and array-specific background noise using only data from within each array. SCAN can be applied to one-channel (e.g., Affymetrix) or two-channel (e.g., Agilent) microarrays. The Universal exPression Codes (UPC) method is an extension of SCAN that estimates whether a given gene/transcript is active above background levels in a given sample. The UPC method can be applied to one-channel or two-channel microarrays as well as to RNA-Seq read counts. Because UPC values are represented on the same scale and have an identical interpretation for each platform, they can be used for cross-platform data integration.
Maintained by Stephen R. Piccolo. Last updated 5 months ago.
immunooncologysoftwaremicroarraypreprocessingrnaseqtwochannelonechannel
47.8 match 3.48 score 15 scriptsbioc
rawrr:Direct Access to Orbitrap Data and Beyond
This package wraps the functionality of the Thermo Fisher Scientic RawFileReader .NET 8.0 assembly. Within the R environment, spectra and chromatograms are represented by S3 objects. The package provides basic functions to download and install the required third-party libraries. The package is developed, tested, and used at the Functional Genomics Center Zurich, Switzerland.
Maintained by Christian Panse. Last updated 3 months ago.
massspectrometryproteomicsmetabolomicsinfrastructuresoftwarefastmass-spectrometrymultiplatformorbitrap-ms
16.4 match 56 stars 8.19 score 23 scripts 2 dependents
promerpr
scanstatistics:Space-Time Anomaly Detection using Scan Statistics
Detection of anomalous space-time clusters using the scan statistics methodology. Focuses on prospective surveillance of data streams, scanning for clusters with ongoing anomalies. Hypothesis testing is made possible by Monte Carlo simulation. Allévius (2018) <doi:10.21105/joss.00515>.
Maintained by Paul Romer Present. Last updated 2 years ago.
24.8 match 1 stars 4.81 score 43 scripts
ropensci
mapscanner:Print Maps, Draw on Them, Scan Them Back in
Enables preparation of maps to be printed and drawn on. Modified maps can then be scanned back in, and hand-drawn marks converted to spatial objects.
Maintained by Mark Padgham. Last updated 1 months ago.
14.5 match 90 stars 7.13 score 2 scriptsbioc
xcms:LC-MS and GC-MS Data Analysis
Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling.
Maintained by Steffen Neumann. Last updated 3 days ago.
immunooncologymassspectrometrymetabolomicsbioconductorfeature-detectionmass-spectrometrypeak-detectioncpp
7.1 match 196 stars 14.31 score 984 scripts 11 dependents
r-hyperspec
hyperSpec:Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)
Comfortable ways to work with hyperspectral data sets, i.e. spatially or time-resolved spectra, or spectra with any other kind of information associated with each of the spectra. The spectra can be data as obtained in XRF, UV/VIS, Fluorescence, AES, NIR, IR, Raman, NMR, MS, etc. More generally, any data that is recorded over a discretized variable, e.g. absorbance = f(wavelength), stored as a vector of absorbance values for discrete wavelengths is suitable.
Maintained by Claudia Beleites. Last updated 10 months ago.
data-wranglinghyperspectralimaginginfrarednmrramanspectroscopyuv-visxrf
11.9 match 16 stars 8.13 score 233 scripts 2 dependents
themains
virustotal:R Client for the VirusTotal API
Use VirusTotal, a Google service that analyzes files and URLs for viruses, worms, trojans etc., provides category of the content hosted by a domain from a variety of prominent services, provides passive DNS information, among other things. See <http://www.virustotal.com> for more information.
Maintained by Gaurav Sood. Last updated 2 years ago.
cybersecurityscan-filestrojansvirustotal
16.4 match 11 stars 5.47 score 18 scripts 1 dependentsbioc
universalmotif:Import, Modify, and Export Motifs with R
Allows for importing most common motif types into R for use by functions provided by other Bioconductor motif-related packages. Motifs can be exported into most major motif formats from various classes as defined by other Bioconductor packages. A suite of motif and sequence manipulation and analysis functions are included, including enrichment, comparison, P-value calculation, shuffling, trimming, higher-order motifs, and others.
Maintained by Benjamin Jean-Marie Tremblay. Last updated 4 months ago.
motifannotationmotifdiscoverydataimportgeneregulationmotif-analysismotif-enrichment-analysissequence-logocpp
7.7 match 28 stars 11.04 score 342 scripts 12 dependents
kuadrat
growR:Implementation of the Vegetation Model ModVege
Run grass growth simulations using a grass growth model based on ModVege (Jouven, M., P. Carrère, and R. Baumont "Model Predicting Dynamics of Biomass, Structure and Digestibility of Herbage in Managed Permanent Pastures. 1. Model Description." (2006) <doi:10.1111/j.1365-2494.2006.00515.x>). The implementation in this package contains a few additions to the above cited version of ModVege, such as simulations of management decisions, and influences of snow cover. As such, the model is fit to simulate grass growth in mountainous regions, such as the Swiss Alps. The package also contains routines for calibrating the model and helpful tools for analysing model outputs and performance.
Maintained by Kevin Kramer. Last updated 7 months ago.
agronomygrassgrasslandmodellingsimulation-modeling
15.6 match 3 stars 5.28 score 14 scripts
csafe-isu
cmcR:An Implementation of the 'Congruent Matching Cells' Method
An open-source implementation of the 'Congruent Matching Cells' method for cartridge case identification as proposed by Song (2013) <https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=911193> as well as an extension of the method proposed by Tong et al. (2015) <doi:10.6028/jres.120.008>. Provides a wide range of pre, inter, and post-processing options when working with cartridge case scan data and their associated comparisons. See the cmcR package website for more details and examples.
Maintained by Joe Zemmels. Last updated 2 years ago.
14.3 match 4 stars 5.68 score 60 scripts
sinnweja
haplo.stats:Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous
Routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: haplo.em(), haplo.glm(), haplo.score(), and haplo.power(); all of which have detailed examples in the vignette.
Maintained by Jason P. Sinnwell. Last updated 6 months ago.
13.4 match 2 stars 5.98 score 96 scripts 12 dependents
igraph
igraph:Network Analysis and Visualization
Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.
Maintained by Kirill Müller. Last updated 14 hours ago.
complex-networksgraph-algorithmsgraph-theorymathematicsnetwork-analysisnetwork-graphfortranlibxml2glpkopenblascpp
3.6 match 582 stars 21.11 score 31k scripts 1.9k dependents
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.
ksslnasisnrcssoilsoil-data-accesssoil-surveysoilwebsqlusda
6.6 match 87 stars 11.34 score 1.0k scripts 1 dependents
apache
arrow:Integration to 'Apache' 'Arrow'
'Apache' 'Arrow' <https://arrow.apache.org/> is a cross-language development platform for in-memory data. It specifies a standardized language-independent columnar memory format for flat and hierarchical data, organized for efficient analytic operations on modern hardware. This package provides an interface to the 'Arrow C++' library.
Maintained by Jonathan Keane. Last updated 1 months ago.
3.9 match 15k stars 19.22 score 10k scripts 81 dependents
rstudio
pointblank:Data Validation and Organization of Metadata for Local and Remote Tables
Validate data in data frames, 'tibble' objects, 'Spark' 'DataFrames', and database tables. Validation pipelines can be made using easily-readable, consecutive validation steps. Upon execution of the validation plan, several reporting options are available. User-defined thresholds for failure rates allow for the determination of appropriate reporting actions. Many other workflows are available including an information management workflow, where the aim is to record, collect, and generate useful information on data tables.
Maintained by Richard Iannone. Last updated 9 days ago.
data-assertionsdata-checkerdata-dictionariesdata-framesdata-inferencedata-managementdata-profilerdata-qualitydata-validationdata-verificationdatabase-tableseasy-to-understandreporting-toolschema-validationtesting-toolsyaml-configuration
6.9 match 932 stars 10.59 score 284 scripts
heike
x3ptools:Tools for Working with 3D Surface Measurements
The x3p file format is specified in ISO standard 5436:2000 to describe 3d surface measurements. 'x3ptools' allows reading, writing and basic modifications to the 3D surface measurements.
Maintained by Heike Hofmann. Last updated 6 months ago.
9.3 match 8 stars 7.48 score 281 scripts 2 dependentsbioc
GWASTools:Tools for Genome Wide Association Studies
Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.
Maintained by Stephanie M. Gogarten. Last updated 5 months ago.
snpgeneticvariabilityqualitycontrolmicroarray
6.6 match 17 stars 10.50 score 396 scripts 5 dependents
camillef-git
HDSpatialScan:Multivariate and Functional Spatial Scan Statistics
Allows to detect spatial clusters of abnormal values on multivariate or functional data. Martin KULLDORFF and Lan HUANG and Kevin KONTY (2009) <doi:10.1186/1476-072X-8-58>, Inkyung JUNG and Ho Jin CHO (2015) <doi:10.1186/s12942-015-0024-6>, Lionel CUCALA and Michael GENIN and Caroline LANIER and Florent OCCELLI (2017) <doi:10.1016/j.spasta.2017.06.001>, Lionel CUCALA and Michael GENIN and Florent OCCELLI and Julien SOULA (2019) <doi:10.1016/j.spasta.2018.10.002>, Camille FREVENT and Mohamed-Salem AHMED and Matthieu MARBAC and Michael GENIN (2021) <doi:10.1016/j.spasta.2021.100550>, Zaineb SMIDA and Lionel CUCALA and Ali GANNOUN and Ghislain Durif (2022) <doi:10.1016/j.csda.2021.107378>, Camille FREVENT and Mohamed-Salem AHMED and Sophie DABO-NIANG and Michael GENIN (2023) <doi:10.1093/jrsssc/qlad017>.
Maintained by Camille FREVENT. Last updated 2 years ago.
67.3 match 1.00 score 4 scripts
rdatatable
data.table:Extension of `data.frame`
Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.
Maintained by Tyson Barrett. Last updated 2 hours ago.
2.5 match 3.7k stars 23.52 score 230k scripts 4.6k dependents
muschellij2
neurohcp:Human 'Connectome' Project Interface
Downloads and reads data from Human 'Connectome' Project <https://db.humanconnectome.org> using Amazon Web Services ('AWS') 'S3' buckets.
Maintained by John Muschelli. Last updated 4 years ago.
10.9 match 9 stars 5.35 score 50 scriptsbioc
Rsamtools:Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.
Maintained by Bioconductor Package Maintainer. Last updated 4 months ago.
dataimportsequencingcoveragealignmentqualitycontrolbioconductor-packagecore-packagecurlbzip2xz-utilszlibcpp
3.8 match 28 stars 15.42 score 3.2k scripts 566 dependents
alexanderrobitzsch
miceadds:Some Additional Multiple Imputation Functions, Especially for 'mice'
Contains functions for multiple imputation which complements existing functionality in R. In particular, several imputation methods for the mice package (van Buuren & Groothuis-Oudshoorn, 2011, <doi:10.18637/jss.v045.i03>) are implemented. Main features of the miceadds package include plausible value imputation (Mislevy, 1991, <doi:10.1007/BF02294457>), multilevel imputation for variables at any level or with any number of hierarchical and non-hierarchical levels (Grund, Luedtke & Robitzsch, 2018, <doi:10.1177/1094428117703686>; van Buuren, 2018, Ch.7, <doi:10.1201/9780429492259>), imputation using partial least squares (PLS) for high dimensional predictors (Robitzsch, Pham & Yanagida, 2016), nested multiple imputation (Rubin, 2003, <doi:10.1111/1467-9574.00217>), substantive model compatible imputation (Bartlett et al., 2015, <doi:10.1177/0962280214521348>), and features for the generation of synthetic datasets (Reiter, 2005, <doi:10.1111/j.1467-985X.2004.00343.x>; Nowok, Raab, & Dibben, 2016, <doi:10.18637/jss.v074.i11>).
Maintained by Alexander Robitzsch. Last updated 16 days ago.
missing-datamultiple-imputationopenblascpp
6.3 match 16 stars 9.16 score 542 scripts 9 dependentsbioc
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.
mirnasequencematchingalignment
8.4 match 5.89 score 52 scripts 1 dependents
molina-valero
FORTLS:Automatic Processing of Terrestrial-Based Technologies Point Cloud Data for Forestry Purposes
Process automation of point cloud data derived from terrestrial-based technologies such as Terrestrial Laser Scanner (TLS) or Mobile Laser Scanner. 'FORTLS' enables (i) detection of trees and estimation of tree-level attributes (e.g. diameters and heights), (ii) estimation of stand-level variables (e.g. density, basal area, mean and dominant height), (iii) computation of metrics related to important forest attributes estimated in Forest Inventories at stand-level, and (iv) optimization of plot design for combining TLS data and field measured data. Documentation about 'FORTLS' is described in Molina-Valero et al. (2022, <doi:10.1016/j.envsoft.2022.105337>).
Maintained by Juan Alberto Molina-Valero. Last updated 3 months ago.
forest-inventoryforest-monitoringlidar-point-cloudcpp
7.8 match 22 stars 6.16 score 11 scriptsbioc
DMRScan:Detection of Differentially Methylated Regions
This package detects significant differentially methylated regions (for both qualitative and quantitative traits), using a scan statistic with underlying Poisson heuristics. The scan statistic will depend on a sequence of window sizes (# of CpGs within each window) and on a threshold for each window size. This threshold can be calculated by three different means: i) analytically using Siegmund et.al (2012) solution (preferred), ii) an important sampling as suggested by Zhang (2008), and a iii) full MCMC modeling of the data, choosing between a number of different options for modeling the dependency between each CpG.
Maintained by Christian M Page. Last updated 5 months ago.
softwaretechnologysequencingwholegenome
9.3 match 2 stars 5.15 score 3 scriptsrstudio
keras3:R Interface to 'Keras'
Interface to 'Keras' <https://keras.io>, a high-level neural networks API. 'Keras' was developed with a focus on enabling fast experimentation, supports both convolution based networks and recurrent networks (as well as combinations of the two), and runs seamlessly on both CPU and GPU devices.
Maintained by Tomasz Kalinowski. Last updated 4 days ago.
3.4 match 845 stars 13.57 score 264 scripts 2 dependentsbioc
spiky:Spike-in calibration for cell-free MeDIP
spiky implements methods and model generation for cfMeDIP (cell-free methylated DNA immunoprecipitation) with spike-in controls. CfMeDIP is an enrichment protocol which avoids destructive conversion of scarce template, making it ideal as a "liquid biopsy," but creating certain challenges in comparing results across specimens, subjects, and experiments. The use of synthetic spike-in standard oligos allows diagnostics performed with cfMeDIP to quantitatively compare samples across subjects, experiments, and time points in both relative and absolute terms.
Maintained by Tim Triche. Last updated 5 months ago.
differentialmethylationdnamethylationnormalizationpreprocessingqualitycontrolsequencing
9.1 match 2 stars 4.90 score 3 scriptsbioc
CGEN:An R package for analysis of case-control studies in genetic epidemiology
This is a package for analysis of case-control data in genetic epidemiology. It provides a set of statistical methods for evaluating gene-environment (or gene-genes) interactions under multiplicative and additive risk models, with or without assuming gene-environment (or gene-gene) independence in the underlying population.
Maintained by Justin Lee. Last updated 5 months ago.
snpmultiplecomparisonclusteringfortran
11.3 match 3.90 score 10 scripts
byandell-sysgen
qtl2ggplot:Data Visualization for QTL Experiments
Functions to plot QTL (quantitative trait loci) analysis results and related diagnostics. Part of 'qtl2', an upgrade of the 'qtl' package to better handle high-dimensional data and complex cross designs.
Maintained by Brian S Yandell. Last updated 1 years ago.
10.7 match 5 stars 3.93 score 17 scriptsbioc
rawDiag:Brings Orbitrap Mass Spectrometry Data to Life; Fast and Colorful
Optimizing methods for liquid chromatography coupled to mass spectrometry (LC-MS) poses a nontrivial challenge. The rawDiag package facilitates rational method optimization by generating MS operator-tailored diagnostic plots of scan-level metadata. The package is designed for use on the R shell or as a Shiny application on the Orbitrap instrument PC.
Maintained by Christian Panse. Last updated 4 months ago.
massspectrometryproteomicsmetabolomicsinfrastructuresoftwareshinyappsfastmass-spectrometrymultiplatformorbitrapvisualization
6.2 match 36 stars 6.71 score 18 scripts
geomorphr
geomorph:Geometric Morphometric Analyses of 2D and 3D Landmark Data
Read, manipulate, and digitize landmark data, generate shape variables via Procrustes analysis for points, curves and surfaces, perform shape analyses, and provide graphical depictions of shapes and patterns of shape variation.
Maintained by Dean Adams. Last updated 1 months ago.
3.4 match 76 stars 12.05 score 700 scripts 6 dependents
entjos
TreeMineR:Tree-Based Scan Statistics
Implementation of unconditional Bernoulli Scan Statistic developed by Kulldorff et al. (2003) <doi:10.1111/1541-0420.00039> for hierarchical tree structures. Tree-based Scan Statistics are an exploratory method to identify event clusters across the space of a hierarchical tree.
Maintained by Joshua P. Entrop. Last updated 7 months ago.
11.9 match 3.40 score 2 scriptsbioc
INTACT:Integrate TWAS and Colocalization Analysis for Gene Set Enrichment Analysis
This package integrates colocalization probabilities from colocalization analysis with transcriptome-wide association study (TWAS) scan summary statistics to implicate genes that may be biologically relevant to a complex trait. The probabilistic framework implemented in this package constrains the TWAS scan z-score-based likelihood using a gene-level colocalization probability. Given gene set annotations, this package can estimate gene set enrichment using posterior probabilities from the TWAS-colocalization integration step.
Maintained by Jeffrey Okamoto. Last updated 5 months ago.
6.9 match 15 stars 5.47 score 13 scriptsbioc
memes:motif matching, comparison, and de novo discovery using the MEME Suite
A seamless interface to the MEME Suite family of tools for motif analysis. 'memes' provides data aware utilities for using GRanges objects as entrypoints to motif analysis, data structures for examining & editing motif lists, and novel data visualizations. 'memes' functions and data structures are amenable to both base R and tidyverse workflows.
Maintained by Spencer Nystrom. Last updated 5 months ago.
dataimportfunctionalgenomicsgeneregulationmotifannotationmotifdiscoverysequencematchingsoftware
4.3 match 49 stars 8.68 score 117 scripts 1 dependentsbioc
hoodscanR:Spatial cellular neighbourhood scanning in R
hoodscanR is an user-friendly R package providing functions to assist cellular neighborhood analysis of any spatial transcriptomics data with single-cell resolution. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. The package can result in cell-level neighborhood annotation output, along with funtions to perform neighborhood colocalization analysis and neighborhood-based cell clustering.
Maintained by Ning Liu. Last updated 1 months ago.
spatialtranscriptomicssinglecellclusteringcpp
6.5 match 4 stars 5.32 score 15 scripts
dannyarends
ctl:Correlated Trait Locus Mapping
Identification and network inference of genetic loci associated with correlation changes in quantitative traits (called correlated trait loci, CTLs). Arends et al. (2016) <doi:10.21105/joss.00087>.
Maintained by Danny Arends. Last updated 1 years ago.
10.4 match 3.31 score 103 scripts
zeileis
exams:Automatic Generation of Exams in R
Automatic generation of exams based on exercises in Markdown or LaTeX format, possibly including R code for dynamic generation of exercise elements. Exercise types include single-choice and multiple-choice questions, arithmetic problems, string questions, and combinations thereof (cloze). Output formats include standalone files (PDF, HTML, Docx, ODT, ...), Moodle XML, QTI 1.2, QTI 2.1, Blackboard, Canvas, OpenOlat, ILIAS, TestVision, Particify, ARSnova, Kahoot!, Grasple, and TCExam. In addition to fully customizable PDF exams, a standardized PDF format (NOPS) is provided that can be printed, scanned, and automatically evaluated.
Maintained by Achim Zeileis. Last updated 3 days ago.
4.2 match 1 stars 8.27 score 872 scripts 5 dependents
sergejruff
Virusparies:Visualize and Process Output from 'VirusHunterGatherer'
A collection of tools for downstream analysis of 'VirusHunterGatherer' output. Processing of hittables and plotting of results, enabling better interpretation, is made easier with the provided functions.
Maintained by Ruff Sergej. Last updated 3 months ago.
bioinformaticsdata-drivendiscoverdiscoveryggplot2graphical-tablehidden-markov-modelhmmlearnplotr-programmingsummary-statisticsvirusvirus-discoveryvirus-scanningvirusgatherervirushuntervirushuntergatherervisualization
7.5 match 1 stars 4.49 score 28 scripts
larssnip
micropan:Microbial Pan-Genome Analysis
A collection of functions for computations and visualizations of microbial pan-genomes.
Maintained by Lars Snipen. Last updated 3 years ago.
5.4 match 21 stars 6.15 score 67 scriptsbioc
multiscan:R package for combining multiple scans
Estimates gene expressions from several laser scans of the same microarray
Maintained by Mizanur Khondoker. Last updated 5 months ago.
8.1 match 4.08 score 2 scripts
bioc
ramwas:Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
A complete toolset for methylome-wide association studies (MWAS). It is specifically designed for data from enrichment based methylation assays, but can be applied to other data as well. The analysis pipeline includes seven steps: (1) scanning aligned reads from BAM files, (2) calculation of quality control measures, (3) creation of methylation score (coverage) matrix, (4) principal component analysis for capturing batch effects and detection of outliers, (5) association analysis with respect to phenotypes of interest while correcting for top PCs and known covariates, (6) annotation of significant findings, and (7) multi-marker analysis (methylation risk score) using elastic net. Additionally, RaMWAS include tools for joint analysis of methlyation and genotype data. This work is published in Bioinformatics, Shabalin et al. (2018) <doi:10.1093/bioinformatics/bty069>.
Maintained by Andrey A Shabalin. Last updated 5 months ago.
dnamethylationsequencingqualitycontrolcoveragepreprocessingnormalizationbatcheffectprincipalcomponentdifferentialmethylationvisualization
5.3 match 10 stars 6.08 score 85 scripts
trinker
sentimentr:Calculate Text Polarity Sentiment
Calculate text polarity sentiment at the sentence level and optionally aggregate by rows or grouping variable(s).
Maintained by Tyler Rinker. Last updated 3 years ago.
amplifierpolaritysentimentsentiment-analysisvalence-shifter
3.3 match 432 stars 9.43 score 680 scripts 2 dependents
dusadrian
admisc:Adrian Dusa's Miscellaneous
Contains functions used across packages 'DDIwR', 'QCA' and 'venn'. Interprets and translates, factorizes and negates SOP - Sum of Products expressions, for both binary and multi-value crisp sets, and extracts information (set names, set values) from those expressions. Other functions perform various other checks if possibly numeric (even if all numbers reside in a character vector) and coerce to numeric, or check if the numbers are whole. It also offers, among many others, a highly versatile recoding routine and some more flexible alternatives to the base functions 'with()' and 'within()'. SOP simplification functions in this package use related minimization from package 'QCA', which is recommended to be installed despite not being listed in the Imports field, due to circular dependency issues.
Maintained by Adrian Dusa. Last updated 4 days ago.
4.0 match 2 stars 7.61 score 20 scripts 92 dependentsbioc
spatzie:Identification of enriched motif pairs from chromatin interaction data
Identifies motifs that are significantly co-enriched from enhancer-promoter interaction data. While enhancer-promoter annotation is commonly used to define groups of interaction anchors, spatzie also supports co-enrichment analysis between preprocessed interaction anchors. Supports BEDPE interaction data derived from genome-wide assays such as HiC, ChIA-PET, and HiChIP. Can also be used to look for differentially enriched motif pairs between two interaction experiments.
Maintained by Jennifer Hammelman. Last updated 5 months ago.
dna3dstructuregeneregulationpeakdetectionepigeneticsfunctionalgenomicsclassificationhictranscription
6.9 match 4.30 score 5 scriptsbioc
ProtGenerics:Generic infrastructure for Bioconductor mass spectrometry packages
S4 generic functions and classes needed by Bioconductor proteomics packages.
Maintained by Laurent Gatto. Last updated 2 months ago.
infrastructureproteomicsmassspectrometrybioconductormass-spectrometrymetabolomics
3.0 match 8 stars 9.43 score 4 scripts 188 dependents
robertschneiderfromuqar
CTRing:Density Profiles of Wood from CT Scan Images
Computerized tomography (CT) can be used to assess certain wood properties when wood disks or logs are scanned. Wood density profiles (i.e. variations of wood density from pith to bark) can yield important information used for studies in forest resource assessment, wood quality and dendrochronology studies. The first step consists in transforming grey values from the scan images to density values. The packages then proposes a unique method to automatically locate the pith by combining an adapted Hough Transform method and a one-dimensional edge detector. Tree ring profiles (average ring density, earlywood and latewood density, ring width and percent latewood for each ring) are then obtained.
Maintained by Robert Schneider. Last updated 6 months ago.
13.9 match 2.00 score 2 scripts
moseleybioinformaticslab
ScanCentricPeakCharacterization:Functionality for Characterizing Peaks in Mass Spectrometry in a Scan-Centric Manner
Provides a functions and classes for detecting, characterizing, and integrating peaks in a scan-centric manner from direct-injection mass spectrometry data.
Maintained by Robert M Flight. Last updated 12 months ago.
8.9 match 3.00 score 1 scriptsbioc
msPurity:Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics
msPurity R package was developed to: 1) Assess the spectral quality of fragmentation spectra by evaluating the "precursor ion purity". 2) Process fragmentation spectra. 3) Perform spectral matching. What is precursor ion purity? -What we call "Precursor ion purity" is a measure of the contribution of a selected precursor peak in an isolation window used for fragmentation. The simple calculation involves dividing the intensity of the selected precursor peak by the total intensity of the isolation window. When assessing MS/MS spectra this calculation is done before and after the MS/MS scan of interest and the purity is interpolated at the recorded time of the MS/MS acquisition. Additionally, isotopic peaks can be removed, low abundance peaks are removed that are thought to have limited contribution to the resulting MS/MS spectra and the isolation efficiency of the mass spectrometer can be used to normalise the intensities used for the calculation.
Maintained by Thomas N. Lawson. Last updated 5 months ago.
massspectrometrymetabolomicssoftwarebioconductor-packagedimsfragmentationlc-mslc-msmsmass-spectrometryprecursor-ion-purity
3.7 match 15 stars 7.03 score 44 scripts
tidyverts
tsibble:Tidy Temporal Data Frames and Tools
Provides a 'tbl_ts' class (the 'tsibble') for temporal data in an data- and model-oriented format. The 'tsibble' provides tools to easily manipulate and analyse temporal data, such as filling in time gaps and aggregating over calendar periods.
Maintained by Earo Wang. Last updated 2 months ago.
1.8 match 538 stars 14.47 score 4.4k scripts 42 dependents
jbdorey
BeeBDC:Occurrence Data Cleaning
Flags and checks occurrence data that are in Darwin Core format. The package includes generic functions and data as well as some that are specific to bees. This package is meant to build upon and be complimentary to other excellent occurrence cleaning packages, including 'bdc' and 'CoordinateCleaner'. This package uses datasets from several sources and particularly from the Discover Life Website, created by Ascher and Pickering (2020). For further information, please see the original publication and package website. Publication - Dorey et al. (2023) <doi:10.1101/2023.06.30.547152> and package website - Dorey et al. (2023) <https://github.com/jbdorey/BeeBDC>.
Maintained by James B. Dorey. Last updated 4 months ago.
4.5 match 3 stars 5.68 score 7 scriptsbyandell-sysgen
qtl2pattern:Pattern Support for 'qtl2' Package
Routines in 'qtl2' to study allele patterns in quantitative trait loci (QTL) mapping over a chromosome. Useful in crosses with more than two alleles to identify how sets of alleles, genetically different strands at the same locus, have different response levels. Plots show profiles over a chromosome. Can handle multiple traits together. See <https://github.com/byandell/qtl2pattern>.
Maintained by Brian S Yandell. Last updated 1 years ago.
8.3 match 1 stars 3.00 score 2 scriptsbioc
RMassBank:Workflow to process tandem MS files and build MassBank records
Workflow to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.
Maintained by RMassBank at Eawag. Last updated 5 months ago.
immunooncologybioinformaticsmassspectrometrymetabolomicssoftwareopenjdk
3.9 match 6.19 score 26 scripts
bioc
limma:Linear Models for Microarray and Omics Data
Data analysis, linear models and differential expression for omics data.
Maintained by Gordon Smyth. Last updated 6 days ago.
exonarraygeneexpressiontranscriptionalternativesplicingdifferentialexpressiondifferentialsplicinggenesetenrichmentdataimportbayesianclusteringregressiontimecoursemicroarraymicrornaarraymrnamicroarrayonechannelproprietaryplatformstwochannelsequencingrnaseqbatcheffectmultiplecomparisonnormalizationpreprocessingqualitycontrolbiomedicalinformaticscellbiologycheminformaticsepigeneticsfunctionalgenomicsgeneticsimmunooncologymetabolomicsproteomicssystemsbiologytranscriptomics
1.8 match 13.81 score 16k scripts 585 dependents
rpolars
polars:Lightning-Fast 'DataFrame' Library
Lightning-fast 'DataFrame' library written in 'Rust'. Convert R data to 'Polars' data and vice versa. Perform fast, lazy, larger-than-memory and optimized data queries. 'Polars' is interoperable with the package 'arrow', as both are based on the 'Apache Arrow' Columnar Format.
Maintained by Soren Welling. Last updated 4 days ago.
2.0 match 499 stars 12.01 score 1.0k scripts 2 dependentsbioc
oligo:Preprocessing tools for oligonucleotide arrays
A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).
Maintained by Benilton Carvalho. Last updated 8 days ago.
microarrayonechanneltwochannelpreprocessingsnpdifferentialexpressionexonarraygeneexpressiondataimportzlib
2.3 match 3 stars 10.42 score 528 scripts 10 dependentsbioc
Spectra:Spectra Infrastructure for Mass Spectrometry Data
The Spectra package defines an efficient infrastructure for storing and handling mass spectrometry spectra and functionality to subset, process, visualize and compare spectra data. It provides different implementations (backends) to store mass spectrometry data. These comprise backends tuned for fast data access and processing and backends for very large data sets ensuring a small memory footprint.
Maintained by RforMassSpectrometry Package Maintainer. Last updated 10 days ago.
infrastructureproteomicsmassspectrometrymetabolomicsbioconductorhacktoberfestmass-spectrometry
1.8 match 41 stars 13.01 score 254 scripts 35 dependents
fboehm
qtl2pleio:Testing Pleiotropy in Multiparental Populations
We implement an adaptation of Jiang & Zeng's (1995) <https://www.genetics.org/content/140/3/1111> likelihood ratio test for testing the null hypothesis of pleiotropy against the alternative hypothesis, two separate quantitative trait loci. The test differs from that in Jiang & Zeng (1995) <https://www.genetics.org/content/140/3/1111> and that in Tian et al. (2016) <doi:10.1534/genetics.115.183624> in that our test accommodates multiparental populations.
Maintained by Frederick J Boehm. Last updated 4 years ago.
multiparental-populationsquantitative-geneticsquantitative-traitcpp
5.3 match 5 stars 4.41 score 26 scripts
tkhrotn
rflexscan:The Flexible Spatial Scan Statistic
Functions for the detection of spatial clusters using the flexible spatial scan statistic developed by Tango and Takahashi (2005) <doi:10.1186/1476-072X-4-11>. This package implements a wrapper for the C routine used in the FleXScan 3.1.2 <https://sites.google.com/site/flexscansoftware/home> developed by Takahashi, Yokoyama, and Tango. For details, see Otani et al. (2021) <doi:10.18637/jss.v099.i13>.
Maintained by Takahiro Otani. Last updated 2 years ago.
7.0 match 4 stars 3.30 score 1 scriptsbioc
MSnbase:Base Functions and Classes for Mass Spectrometry and Proteomics
MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.
Maintained by Laurent Gatto. Last updated 2 days ago.
immunooncologyinfrastructureproteomicsmassspectrometryqualitycontroldataimportbioconductorbioinformaticsmass-spectrometryproteomics-datavisualisationcpp
1.8 match 130 stars 12.81 score 772 scripts 36 dependentsbioc
PWMEnrich:PWM enrichment analysis
A toolkit of high-level functions for DNA motif scanning and enrichment analysis built upon Biostrings. The main functionality is PWM enrichment analysis of already known PWMs (e.g. from databases such as MotifDb), but the package also implements high-level functions for PWM scanning and visualisation. The package does not perform "de novo" motif discovery, but is instead focused on using motifs that are either experimentally derived or computationally constructed by other tools.
Maintained by Diego Diez. Last updated 5 months ago.
motifannotationsequencematchingsoftware
4.3 match 5.08 score 60 scripts
juba
questionr:Functions to Make Surveys Processing Easier
Set of functions to make the processing and analysis of surveys easier : interactive shiny apps and addins for data recoding, contingency tables, dataset metadata handling, and several convenience functions.
Maintained by Julien Barnier. Last updated 1 days ago.
1.7 match 83 stars 12.62 score 1.1k scripts 19 dependentsbioc
VariantAnnotation:Annotation of Genetic Variants
Annotate variants, compute amino acid coding changes, predict coding outcomes.
Maintained by Bioconductor Package Maintainer. Last updated 2 months ago.
dataimportsequencingsnpannotationgeneticsvariantannotationcurlbzip2xz-utilszlib
1.9 match 11.39 score 1.9k scripts 152 dependentsbioc
coMET:coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns
Visualisation of EWAS results in a genomic region. In addition to phenotype-association P-values, coMET also generates plots of co-methylation patterns and provides a series of annotation tracks. It can be used to other omic-wide association scans as lon:g as the data can be translated to genomic level and for any species.
Maintained by Tiphaine Martin. Last updated 2 days ago.
softwaredifferentialmethylationvisualizationsequencinggeneticsfunctionalgenomicsmicroarraymethylationarraymethylseqchipseqdnaseqriboseqrnaseqexomeseqdnamethylationgenomewideassociationmotifannotation
4.8 match 4.41 score 17 scriptsbioc
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.
motifannotationgeneregulationmotifdiscoverytranscriptionalignment
1.7 match 28 stars 12.36 score 1.1k scripts 18 dependents
ahgroup
DSAIRM:Dynamical Systems Approach to Immune Response Modeling
Simulation models (apps) of various within-host immune response scenarios. The purpose of the package is to help individuals learn about within-host infection and immune response modeling from a dynamical systems perspective. All apps include explanations of the underlying models and instructions on what to do with the models.
Maintained by Andreas Handel. Last updated 8 months ago.
3.4 match 34 stars 6.19 score 23 scripts
cran
rehh.data:Data Only: Searching for Footprints of Selection using Haplotype Homozygosity Based Tests
Contains example data for the 'rehh' package.
Maintained by Mathieu Gautier. Last updated 8 years ago.
6.8 match 3.06 score 19 scripts 2 dependents
sonatype-nexus-community
oysteR:Scans R Projects for Vulnerable Third Party Dependencies
Collects a list of your third party R packages, and scans them with the 'OSS' Index provided by 'Sonatype', reporting back on any vulnerabilities that are found in the third party packages you use.
Maintained by Colin Gillespie. Last updated 4 years ago.
3.4 match 40 stars 6.08 score 6 scripts
erickawaguchi
fastcmprsk:Fine-Gray Regression via Forward-Backward Scan
In competing risks regression, the proportional subdistribution hazards (PSH) model is popular for its direct assessment of covariate effects on the cumulative incidence function. This package allows for both penalized and unpenalized PSH regression in linear time using a novel forward-backward scan. Penalties include Ridge, Lease Absolute Shrinkage and Selection Operator (LASSO), Smoothly Clipped Absolute Deviation (SCAD), Minimax Concave Plus (MCP), and elastic net <doi: 10.32614/RJ-2021-010>.
Maintained by Eric S. Kawaguchi. Last updated 5 months ago.
5.0 match 4 stars 3.88 score 19 scripts
umr-amap
AMAPVox:LiDAR Data Voxelisation
Read, manipulate and write voxel spaces. Voxel spaces are read from text-based output files of the 'AMAPVox' software. 'AMAPVox' is a LiDAR point cloud voxelisation software that aims at estimating leaf area through several theoretical/numerical approaches. See more in the article Vincent et al. (2017) <doi:10.23708/1AJNMP> and the technical note Vincent et al. (2021) <doi:10.23708/1AJNMP>.
Maintained by Philippe Verley. Last updated 2 months ago.
3.0 match 15 stars 6.35 score 12 scripts
thomaschln
snplinkage:Single Nucleotide Polymorphisms Linkage Disequilibrium Visualizations
Linkage disequilibrium visualizations of up to several hundreds of single nucleotide polymorphisms (SNPs), annotated with chromosomic positions and gene names. Two types of plots are available for small numbers of SNPs (<40) and for large numbers (tested up to 500). Both can be extended by combining other ggplots, e.g. association studies results, and functions enable to directly visualize the effect of SNP selection methods, as minor allele frequency filtering and TagSNP selection, with a second correlation heatmap. The SNPs correlations are computed on Genotype Data objects from the 'GWASTools' package using the 'SNPRelate' package, and the plots are customizable 'ggplot2' and 'gtable' objects and are annotated using the 'biomaRt' package. Usage is detailed in the vignette with example data and results from up to 500 SNPs of 1,200 scans are in Charlon T. (2019) <doi:10.13097/archive-ouverte/unige:161795>.
Maintained by Thomas Charlon. Last updated 4 months ago.
geneticvariabilitymicroarraysnp
4.1 match 4.62 score 14 scripts
pakillo
grateful:Facilitate Citation of R Packages
Facilitates the citation of R packages used in analysis projects. Scans project for packages used, gets their citations, and produces a document with citations in the preferred bibliography format, ready to be pasted into reports or manuscripts. Alternatively, 'grateful' can be used directly within an 'R Markdown' or 'Quarto' document.
Maintained by Francisco Rodriguez-Sanchez. Last updated 3 days ago.
citation-generatorsoftware-citation
2.3 match 229 stars 8.04 score 269 scriptscran
scbursts:Single Channel Bursts Analysis
Provides tools to import and export from several existing pieces of ion-channel analysis software such as 'TAC', 'QUB', 'SCAN', and 'Clampfit', implements procedures such as dwell-time correction and defining bursts with a critical time, and provides tools for analysis of bursts, such as tools for sorting and plotting.
Maintained by Blair Drummond. Last updated 6 years ago.
9.3 match 2.00 scorebioc
TFutils:TFutils
This package helps users to work with TF metadata from various sources. Significant catalogs of TFs and classifications thereof are made available. Tools for working with motif scans are also provided.
Maintained by Vincent Carey. Last updated 4 months ago.
3.8 match 4.80 score 21 scripts
opengeos
whitebox:'WhiteboxTools' R Frontend
An R frontend for the 'WhiteboxTools' library, which is an advanced geospatial data analysis platform developed by Prof. John Lindsay at the University of Guelph's Geomorphometry and Hydrogeomatics Research Group. 'WhiteboxTools' can be used to perform common geographical information systems (GIS) analysis operations, such as cost-distance analysis, distance buffering, and raster reclassification. Remote sensing and image processing tasks include image enhancement (e.g. panchromatic sharpening, contrast adjustments), image mosaicing, numerous filtering operations, simple classification (k-means), and common image transformations. 'WhiteboxTools' also contains advanced tooling for spatial hydrological analysis (e.g. flow-accumulation, watershed delineation, stream network analysis, sink removal), terrain analysis (e.g. common terrain indices such as slope, curvatures, wetness index, hillshading; hypsometric analysis; multi-scale topographic position analysis), and LiDAR data processing. Suggested citation: Lindsay (2016) <doi:10.1016/j.cageo.2016.07.003>.
Maintained by Andrew Brown. Last updated 5 months ago.
geomorphometrygeoprocessinggeospatialgishydrologyremote-sensingrstudio
1.9 match 173 stars 9.65 score 203 scripts 2 dependents
r-lib
pkgdepends:Package Dependency Resolution and Downloads
Find recursive dependencies of 'R' packages from various sources. Solve the dependencies to obtain a consistent set of packages to install. Download packages, and install them. It supports packages on 'CRAN', 'Bioconductor' and other 'CRAN-like' repositories, 'GitHub', package 'URLs', and local package trees and files. It caches metadata and package files via the 'pkgcache' package, and performs all 'HTTP' requests, downloads, builds and installations in parallel. 'pkgdepends' is the workhorse of the 'pak' package.
Maintained by Gábor Csárdi. Last updated 17 days ago.
1.8 match 110 stars 9.89 score 67 scripts 5 dependents
kharchenkolab
conos:Clustering on Network of Samples
Wires together large collections of single-cell RNA-seq datasets, which allows for both the identification of recurrent cell clusters and the propagation of information between datasets in multi-sample or atlas-scale collections. 'Conos' focuses on the uniform mapping of homologous cell types across heterogeneous sample collections. For instance, users could investigate a collection of dozens of peripheral blood samples from cancer patients combined with dozens of controls, which perhaps includes samples of a related tissue such as lymph nodes. This package interacts with data available through the 'conosPanel' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/conos>. The size of the 'conosPanel' package is approximately 12 MB.
Maintained by Evan Biederstedt. Last updated 1 years ago.
batch-correctionscrna-seqsingle-cell-rna-seqopenblascppopenmp
2.4 match 204 stars 7.32 score 258 scripts
aphalo
rOmniDriver:Omni Driver R wrapper
This package is a wrapper of the OmniDriver java driver for Ocean Optics spectrometers.
Maintained by Pedro J. Aphalo. Last updated 7 months ago.
data-acquisitionspectroscopyopenjdk
5.8 match 1 stars 3.00 score 6 scripts
natverse
nat:NeuroAnatomy Toolbox for Analysis of 3D Image Data
NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D biological image data, especially traced neurons. Reads and writes 3D images in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf format. Traced neurons can be imported from and written to SWC and 'Amira' LineSet and SkeletonGraph formats. These data can then be visualised in 3D via 'rgl', manipulated including applying calculated registrations, e.g. using the 'CMTK' registration suite, and analysed. There is also a simple representation for neurons that have been subjected to 3D skeletonisation but not formally traced; this allows morphological comparison between neurons including searches and clustering (via the 'nat.nblast' extension package).
Maintained by Gregory Jefferis. Last updated 5 months ago.
3dconnectomicsimage-analysisneuroanatomyneuroanatomy-toolboxneuronneuron-morphologyneurosciencevisualisation
1.7 match 67 stars 9.94 score 436 scripts 2 dependentsbioc
seqPattern:Visualising oligonucleotide patterns and motif occurrences across a set of sorted sequences
Visualising oligonucleotide patterns and sequence motifs occurrences across a large set of sequences centred at a common reference point and sorted by a user defined feature.
Maintained by Vanja Haberle. Last updated 5 months ago.
3.5 match 4.78 score 12 scripts 7 dependents
richfitz
redux:R Bindings to 'hiredis'
A 'hiredis' wrapper that includes support for transactions, pipelining, blocking subscription, serialisation of all keys and values, 'Redis' error handling with R errors. Includes an automatically generated 'R6' interface to the full 'hiredis' API. Generated functions are faithful to the 'hiredis' documentation while attempting to match R's argument semantics. Serialisation must be explicitly done by the user, but both binary and text-mode serialisation is supported.
Maintained by Rich FitzJohn. Last updated 1 years ago.
1.9 match 95 stars 8.95 score 41 scripts 9 dependentsbioc
MsQuality:MsQuality - Quality metric calculation from Spectra and MsExperiment objects
The MsQuality provides functionality to calculate quality metrics for mass spectrometry-derived, spectral data at the per-sample level. MsQuality relies on the mzQC framework of quality metrics defined by the Human Proteom Organization-Proteomics Standards Initiative (HUPO-PSI). These metrics quantify the quality of spectral raw files using a controlled vocabulary. The package is especially addressed towards users that acquire mass spectrometry data on a large scale (e.g. data sets from clinical settings consisting of several thousands of samples). The MsQuality package allows to calculate low-level quality metrics that require minimum information on mass spectrometry data: retention time, m/z values, and associated intensities. MsQuality relies on the Spectra package, or alternatively the MsExperiment package, and its infrastructure to store spectral data.
Maintained by Thomas Naake. Last updated 2 months ago.
metabolomicsproteomicsmassspectrometryqualitycontrolmass-spectrometryqc
3.1 match 7 stars 5.45 score 2 scriptsrstudio
tfdatasets:Interface to 'TensorFlow' Datasets
Interface to 'TensorFlow' Datasets, a high-level library for building complex input pipelines from simple, re-usable pieces. See <https://www.tensorflow.org/guide> for additional details.
Maintained by Tomasz Kalinowski. Last updated 5 days ago.
1.8 match 34 stars 9.32 score 656 scripts 3 dependentsaphalo
photobiologyInOut:Read Spectral and Logged Data from Foreign Files
Functions for reading, and in some cases writing, foreign files containing spectral data from spectrometers and their associated software, output from daylight simulation models in common use, and some spectral data repositories. As well as functions for exchange of spectral data with other R packages. Part of the 'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Maintained by Pedro J. Aphalo. Last updated 17 days ago.
2.5 match 6.32 score 63 scripts 1 dependents
icarda-git
QBMS:Query the Breeding Management System(s)
This R package assists breeders in linking data systems with their analytic pipelines, a crucial step in digitizing breeding processes. It supports querying and retrieving phenotypic and genotypic data from systems like 'EBS' <https://ebs.excellenceinbreeding.org/>, 'BMS' <https://bmspro.io>, 'BreedBase' <https://breedbase.org>, and 'GIGWA' <https://github.com/SouthGreenPlatform/Gigwa2> (using 'BrAPI' <https://brapi.org> calls). Extra helper functions support environmental data sources, including 'TerraClimate' <https://www.climatologylab.org/terraclimate.html> and 'FAO' 'HWSDv2' <https://gaez.fao.org/pages/hwsd> soil database.
Maintained by Khaled Al-Shamaa. Last updated 6 months ago.
2.0 match 8 stars 7.85 score 33 scripts 1 dependents
lightbluetitan
OncoDataSets:A Comprehensive Collection of Cancer Types and Cancer-related DataSets
Offers a rich collection of data focused on cancer research, covering survival rates, genetic studies, biomarkers, and epidemiological insights. Designed for researchers, analysts, and bioinformatics practitioners, the package includes datasets on various cancer types such as melanoma, leukemia, breast, ovarian, and lung cancer, among others. It aims to facilitate advanced research, analysis, and understanding of cancer epidemiology, genetics, and treatment outcomes.
Maintained by Renzo Caceres Rossi. Last updated 3 months ago.
3.8 match 3 stars 4.18 score 6 scripts
bioc
SpatialOmicsOverlay:Spatial Overlay for Omic Data from Nanostring GeoMx Data
Tools for NanoString Technologies GeoMx Technology. Package to easily graph on top of an OME-TIFF image. Plotting annotations can range from tissue segment to gene expression.
Maintained by Maddy Griswold. Last updated 5 months ago.
geneexpressiontranscriptioncellbasedassaysdataimporttranscriptomicsproteomicsproprietaryplatformsrnaseqspatialdatarepresentationvisualizationopenjdk
3.5 match 4.30 score 8 scripts
troyhill
coreCT:Programmatic Analysis of Sediment Cores Using Computed Tomography Imaging
Computed tomography (CT) imaging is a powerful tool for understanding the composition of sediment cores. This package streamlines and accelerates the analysis of CT data generated in the context of environmental science. Included are tools for processing raw DICOM images to characterize sediment composition (sand, peat, etc.). Root analyses are also enabled, including measures of external surface area and volumes for user-defined root size classes. For a detailed description of the application of computed tomography imaging for sediment characterization, see: Davey, E., C. Wigand, R. Johnson, K. Sundberg, J. Morris, and C. Roman. (2011) <DOI: 10.1890/10-2037.1>.
Maintained by Troy D. Hill. Last updated 4 years ago.
biomasscomputed-tomographysedimentsediment-core
3.4 match 3 stars 4.41 score 17 scripts
squ4reanalytics
D4TAlink.light:FAIR Data - Workflow Management
Tools, methods and processes for the management of analysis workflows. These lightweight solutions facilitate structuring R&D activities. These solutions were developed to comply with Good Documentation Practice (GDP), with FAIR principles as discussed by Jacobsen et al. (2017) <doi:10.1162/dint_r_00024>, and with ALCOA+ principles as proposed by the U.S. FDA.
Maintained by Gregoire Thomas. Last updated 4 months ago.
3.4 match 4.30 scorebioc
protGear:Protein Micro Array Data Management and Interactive Visualization
A generic three-step pre-processing package for protein microarray data. This package contains different data pre-processing procedures to allow comparison of their performance.These steps are background correction, the coefficient of variation (CV) based filtering, batch correction and normalization.
Maintained by Kennedy Mwai. Last updated 5 months ago.
microarrayonechannelpreprocessingbiomedicalinformaticsproteomicsbatcheffectnormalizationbayesianclusteringregressionsystemsbiologyimmunooncologybackground-correctionmicroarray-datanormalisationproteomics-datashinyshinydashboard
3.4 match 1 stars 4.30 score 6 scriptsropensci
UCSCXenaTools:Download and Explore Datasets from UCSC Xena Data Hubs
Download and explore datasets from UCSC Xena data hubs, which are a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others. Databases are normalized so they can be combined, linked, filtered, explored and downloaded.
Maintained by Shixiang Wang. Last updated 5 months ago.
api-clientbioinformaticsccledownloadericgctcgatoiltreehouseucscucsc-xena
1.7 match 106 stars 8.55 score 163 scripts 1 dependents
f8l5h9
spqdep:Testing for Spatial Independence of Cross-Sectional Qualitative Data
Testing for Spatial Dependence of Qualitative Data in Cross Section. The list of functions includes join-count tests, Q test, spatial scan test, similarity test and spatial runs test. The methodology of these models can be found in <doi:10.1007/s10109-009-0100-1> and <doi:10.1080/13658816.2011.586327>.
Maintained by Fernando Lopez. Last updated 3 months ago.
categorical-dataqualitative-analysisspatial-data-analysisspatial-econometricsstatistical-tests
4.8 match 3.00 score 3 scriptsjfrench
smacpod:Statistical Methods for the Analysis of Case-Control Point Data
Statistical methods for analyzing case-control point data. Methods include the ratio of kernel densities, the difference in K Functions, the spatial scan statistic, and q nearest neighbors of cases.
Maintained by Joshua French. Last updated 5 months ago.
3.9 match 3.69 score 49 scriptsbioc
OncoScore:A tool to identify potentially oncogenic genes
OncoScore is a tool to measure the association of genes to cancer based on citation frequencies in biomedical literature. The score is evaluated from PubMed literature by dynamically updatable web queries.
Maintained by Luca De Sano. Last updated 5 months ago.
2.3 match 5 stars 6.15 score 2 scripts
dankelley
plan:Tools for Project Planning
Supports the creation of 'burndown' charts and 'gantt' diagrams.
Maintained by Dan Kelley. Last updated 2 years ago.
1.9 match 33 stars 7.23 score 103 scriptsropensci
restez:Create and Query a Local Copy of 'GenBank' in R
Download large sections of 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> and generate a local SQL-based database. A user can then query this database using 'restez' functions or through 'rentrez' <https://CRAN.R-project.org/package=rentrez> wrappers.
Maintained by Joel H. Nitta. Last updated 10 days ago.
1.9 match 26 stars 7.01 score 175 scripts 1 dependents
lm186
MRS:Multi-Resolution Scanning for Cross-Sample Differences
An implementation of the MRS algorithm for comparison across distributions, as described in Jacopo Soriano, Li Ma (2017) <doi:10.1111/rssb.12180>. The model is based on a nonparametric process taking the form of a Markov model that transitions between a "null" and an "alternative" state on a multi-resolution partition tree of the sample space. MRS effectively detects and characterizes a variety of underlying differences. These differences can be visualized using several plotting functions.
Maintained by Li Ma. Last updated 1 years ago.
6.5 match 2.00 score 7 scriptsbioc
GENESIS:GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
The GENESIS package provides methodology for estimating, inferring, and accounting for population and pedigree structure in genetic analyses. The current implementation provides functions to perform PC-AiR (Conomos et al., 2015, Gen Epi) and PC-Relate (Conomos et al., 2016, AJHG). PC-AiR performs a Principal Components Analysis on genome-wide SNP data for the detection of population structure in a sample that may contain known or cryptic relatedness. Unlike standard PCA, PC-AiR accounts for relatedness in the sample to provide accurate ancestry inference that is not confounded by family structure. PC-Relate uses ancestry representative principal components to adjust for population structure/ancestry and accurately estimate measures of recent genetic relatedness such as kinship coefficients, IBD sharing probabilities, and inbreeding coefficients. Additionally, functions are provided to perform efficient variance component estimation and mixed model association testing for both quantitative and binary phenotypes.
Maintained by Stephanie M. Gogarten. Last updated 1 months ago.
snpgeneticvariabilitygeneticsstatisticalmethoddimensionreductionprincipalcomponentgenomewideassociationqualitycontrolbiocviews
1.3 match 36 stars 10.44 score 342 scripts 1 dependents
isoverse
isoorbi:Process Orbitrap Isotopocule Data
Read and process isotopocule data from an Orbitrap Isotope Solutions mass spectrometer. Citation: Kantnerova et al. (Nature Protocols, 2024).
Maintained by Caj Neubauer. Last updated 7 months ago.
2.0 match 4 stars 6.31 score 17 scripts
al-obrien
rosv:Client to Access and Operate on the 'Open Source Vulnerability' API
Connect, query, and operate on information available from the 'Open Source Vulnerability' database <https://osv.dev/>. Although 'CRAN' has vulnerabilities listed, these are few compared to projects such as 'PyPI'. With tighter integration between 'R' and 'Python', having an 'R' specific package to access details about vulnerabilities from various sources is a worthwhile enterprise.
Maintained by Allen OBrien. Last updated 7 months ago.
3.1 match 2 stars 4.00 score 7 scripts
tombishop1
itraxR:Itrax Data Analysis Tools
Parse, trim, join, visualise and analyse data from Itrax sediment core multi-parameter scanners manufactured by Cox Analytical Systems, Sweden. Functions are provided for parsing XRF-peak area files, line-scan optical images, and radiographic images, alongside accompanying metadata. A variety of data wrangling tasks like trimming, joining and reducing XRF-peak area data are simplified. Multivariate methods are implemented with appropriate data transformation.
Maintained by Thomas Bishop. Last updated 10 months ago.
4.1 match 5 stars 3.00 score 1 scriptsbioc
CNEr:CNE Detection and Visualization
Large-scale identification and advanced visualization of sets of conserved noncoding elements.
Maintained by Ge Tan. Last updated 5 months ago.
generegulationvisualizationdataimport
1.3 match 3 stars 9.28 score 35 scripts 19 dependents
epiverse-trace
cleanepi:Clean and Standardize Epidemiological Data
Cleaning and standardizing tabular data package, tailored specifically for curating epidemiological data. It streamlines various data cleaning tasks that are typically expected when working with datasets in epidemiology. It returns the processed data in the same format, and generates a comprehensive report detailing the outcomes of each cleaning task.
Maintained by Karim Mané. Last updated 3 days ago.
data-cleaningepidemiologyepiverse
1.6 match 9 stars 7.44 score 19 scripts
patzaw
TKCat:Tailored Knowledge Catalog
Facilitate the management of data from knowledge resources that are frequently used alone or together in research environments. In 'TKCat', knowledge resources are manipulated as modeled database (MDB) objects. These objects provide access to the data tables along with a general description of the resource and a detail data model documenting the tables, their fields and their relationships. These MDBs are then gathered in catalogs that can be easily explored an shared. Finally, 'TKCat' provides tools to easily subset, filter and combine MDBs and create new catalogs suited for specific needs.
Maintained by Patrice Godard. Last updated 2 days ago.
2.0 match 5 stars 6.08 score 27 scripts
masterclm
mclm:Mastering Corpus Linguistics Methods
Read, inspect and process corpus files for quantitative corpus linguistics. Obtain concordances via regular expressions, tokenize texts, and compute frequencies and association measures. Useful for collocation analysis, keywords analysis and variationist studies (comparison of linguistic variants and of linguistic varieties).
Maintained by Mariana Montes. Last updated 2 years ago.
3.8 match 1 stars 3.24 score 35 scripts
brauckhoff
biopixR:Extracting Insights from Biological Images
Combines the 'magick' and 'imager' packages to streamline image analysis, focusing on feature extraction and quantification from biological images, especially microparticles. By providing high throughput pipelines and clustering capabilities, 'biopixR' facilitates efficient insight generation for researchers (Schneider J. et al. (2019) <doi:10.21037/jlpm.2019.04.05>).
Maintained by Tim Brauckhoff. Last updated 4 months ago.
1.9 match 5 stars 6.36 score 23 scripts
pik-piam
citation:Software Citation Tools
A collection of functions to extract citation information from 'R' packages and to deal with files in 'citation file format' (<https://citation-file-format.github.io/>), extending the functionality already provided by the citation() function in the 'utils' package.
Maintained by Jan Philipp Dietrich. Last updated 3 months ago.
2.3 match 1 stars 5.30 score 11 scripts 10 dependentskbroman
qtlcharts:Interactive Graphics for QTL Experiments
Web-based interactive charts (using D3.js) for the analysis of experimental crosses to identify genetic loci (quantitative trait loci, QTL) contributing to variation in quantitative traits. Broman (2015) <doi:10.1534/genetics.114.172742>.
Maintained by Karl W Broman. Last updated 2 years ago.
1.8 match 84 stars 6.61 score 322 scriptsbioc
ATACseqQC:ATAC-seq Quality Control
ATAC-seq, an assay for Transposase-Accessible Chromatin using sequencing, is a rapid and sensitive method for chromatin accessibility analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq and DNAse-seq. Comparing to the other methods, ATAC-seq requires less amount of the biological samples and time to process. In the process of analyzing several ATAC-seq dataset produced in our labs, we learned some of the unique aspects of the quality assessment for ATAC-seq data.To help users to quickly assess whether their ATAC-seq experiment is successful, we developed ATACseqQC package partially following the guideline published in Nature Method 2013 (Greenleaf et al.), including diagnostic plot of fragment size distribution, proportion of mitochondria reads, nucleosome positioning pattern, and CTCF or other Transcript Factor footprints.
Maintained by Jianhong Ou. Last updated 2 months ago.
sequencingdnaseqatacseqgeneregulationqualitycontrolcoveragenucleosomepositioningimmunooncology
1.7 match 7.12 score 146 scripts 1 dependentsbioc
beadarray:Quality assessment and low-level analysis for Illumina BeadArray data
The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.
Maintained by Mark Dunning. Last updated 5 months ago.
microarrayonechannelqualitycontrolpreprocessing
1.5 match 7.88 score 70 scripts 4 dependents
uribo
ssrn:Scan Statistics for Railway Network
Implement the algorithm provided in scan for estimating the transmission route on railway network using passenger volume. It is a generalization of the scan statistic approach for railway network to identify the hot railway route for transmitting infectious diseases.
Maintained by Shinya Uryu. Last updated 5 years ago.
3.9 match 2 stars 3.00 score 5 scripts
microsoft
wpa:Tools for Analysing and Visualising Viva Insights Data
Opinionated functions that enable easier and faster analysis of Viva Insights data. There are three main types of functions in 'wpa': (i) Standard functions create a 'ggplot' visual or a summary table based on a specific Viva Insights metric; (2) Report Generation functions generate HTML reports on a specific analysis area, e.g. Collaboration; (3) Other miscellaneous functions cover more specific applications (e.g. Subject Line text mining) of Viva Insights data. This package adheres to 'tidyverse' principles and works well with the pipe syntax. 'wpa' is built with the beginner-to-intermediate R users in mind, and is optimised for simplicity.
Maintained by Martin Chan. Last updated 4 months ago.
1.8 match 30 stars 6.69 score 39 scripts 1 dependents
marsdu1989
FlexScan:Flexible Scan Statistics
An easy way to conduct flexible scan. Monte-Carlo method is used to test the spatial clusters given the cases, population, and shapefile. A table with formal style and a map with clusters are included in the result report. The method can be referenced at: Toshiro Tango and Kunihiko Takahashi (2005) <doi:10.1186/1476-072X-4-11>.
Maintained by Zhicheng Du. Last updated 3 years ago.
5.8 match 2.00 score 2 scriptscran
episcan:Scan Pairwise Epistasis
Searching genomic interactions with linear/logistic regression in a high-dimensional dataset is a time-consuming task. This package provides some efficient ways to scan epistasis in genome-wide interaction studies (GWIS). Both case-control status (binary outcome) and quantitative phenotype (continuous outcome) are supported (the main references: 1. Kam-Thong, T., D. Czamara, K. Tsuda, K. Borgwardt, C. M. Lewis, A. Erhardt-Lehmann, B. Hemmer, et al. (2011). <doi:10.1038/ejhg.2010.196>. 2. Kam-Thong, T., B. Pütz, N. Karbalai, B. Müller-Myhsok, and K. Borgwardt. (2011). <doi:10.1093/bioinformatics/btr218>.)
Maintained by Beibei Jiang. Last updated 7 years ago.
5.8 match 2.00 score
yeyuan98
clockSim:Simulation of the Circadian Clock Gene Network
A preconfigured simulation workflow for the circadian clock gene network.
Maintained by Ye Yuan. Last updated 7 days ago.
4.1 match 2.78 score 3 scriptscran
incidental:Implements Empirical Bayes Incidence Curves
Make empirical Bayes incidence curves from reported case data using a specified delay distribution.
Maintained by Lauren Hannah. Last updated 5 years ago.
3.8 match 2 stars 3.00 score 10 scriptsbioc
aroma.light:Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types
Methods for microarray analysis that take basic data types such as matrices and lists of vectors. These methods can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes.
Maintained by Henrik Bengtsson. Last updated 5 months ago.
infrastructuremicroarrayonechanneltwochannelmultichannelvisualizationpreprocessingbioconductor
1.7 match 1 stars 6.43 score 26 scripts 20 dependents
raim
dpseg:Piecewise Linear Segmentation by Dynamic Programming
Piecewise linear segmentation of ordered data by a dynamic programming algorithm. The algorithm was developed for time series data, e.g. growth curves, and for genome-wide read-count data from next generation sequencing, but is broadly applicable. Generic implementations of dynamic programming routines allow to scan for optimal segmentation parameters and test custom segmentation criteria ("scoring functions").
Maintained by Rainer Machne. Last updated 26 days ago.
2.3 match 4.71 score 17 scripts 1 dependents
steve-the-bayesian
Boom:Bayesian Object Oriented Modeling
A C++ library for Bayesian modeling, with an emphasis on Markov chain Monte Carlo. Although boom contains a few R utilities (mainly plotting functions), its primary purpose is to install the BOOM C++ library on your system so that other packages can link against it.
Maintained by Steven L. Scott. Last updated 1 years ago.
2.3 match 9 stars 4.82 score 57 scripts 6 dependentsahgroup
DSAIDE:Dynamical Systems Approach to Infectious Disease Epidemiology (Ecology/Evolution)
Exploration of simulation models (apps) of various infectious disease transmission dynamics scenarios. The purpose of the package is to help individuals learn about infectious disease epidemiology (ecology/evolution) from a dynamical systems perspective. All apps include explanations of the underlying models and instructions on what to do with the models.
Maintained by Andreas Handel. Last updated 1 years ago.
1.7 match 26 stars 6.30 score 22 scriptsbioc
DEScan2:Differential Enrichment Scan 2
Integrated peak and differential caller, specifically designed for broad epigenomic signals.
Maintained by Dario Righelli. Last updated 5 months ago.
immunooncologypeakdetectionepigeneticssoftwaresequencingcoveragecpp
3.1 match 3.30 score 2 scriptsbioc
fcScan:fcScan for detecting clusters of coordinates with user defined options
This package is used to detect combination of genomic coordinates falling within a user defined window size along with user defined overlap between identified neighboring clusters. It can be used for genomic data where the clusters are built on a specific chromosome or specific strand. Clustering can be performed with a "greedy" option allowing thus the presence of additional sites within the allowed window size.
Maintained by Pierre Khoueiry. Last updated 5 months ago.
3.1 match 3.30 score 1 scripts
pbourkey
polyqtlR:QTL Analysis in Autopolyploid Bi-Parental F1 Populations
Quantitative trait loci (QTL) analysis and exploration of meiotic patterns in autopolyploid bi-parental F1 populations. For all ploidy levels, identity-by-descent (IBD) probabilities can be estimated. Significance thresholds, exploring QTL allele effects and visualising results are provided. For more background and to reference the package see <doi:10.1093/bioinformatics/btab574>.
Maintained by Peter Bourke. Last updated 1 years ago.
4.5 match 2.30 score 2 scriptscran
GenoScan:A Genome-Wide Scan Statistic Framework for Whole-Genome Sequence Data Analysis
Functions for whole-genome sequencing studies, including genome-wide scan, candidate region scan and single window test.
Maintained by Zihuai He. Last updated 6 years ago.
10.0 match 1.00 scorecran
WGScan:A Genome-Wide Scan Statistic Framework for Whole-Genome Sequence Data Analysis
Functions for the analysis of whole-genome sequencing studies to simultaneously detect the existence, and estimate the locations of association signals at genome-wide scale. The functions allow genome-wide association scan, candidate region scan and single window test.
Maintained by Zihuai He. Last updated 6 years ago.
10.0 match 1.00 scorebioc
scanMiRApp:scanMiR shiny application
A shiny interface to the scanMiR package. The application enables the scanning of transcripts and custom sequences for miRNA binding sites, the visualization of KdModels and binding results, as well as browsing predicted repression data. In addition contains the IndexedFst class for fast indexed reading of large GenomicRanges or data.frames, and some utilities for facilitating scans and identifying enriched miRNA-target pairs.
Maintained by Pierre-Luc Germain. Last updated 5 months ago.
mirnasequencematchingguishinyapps
2.0 match 4.88 score 19 scripts
benbruyneel
proteinDiscover:ProteinDiscover
Provides an interface to the data contained in Proteome Discoverer (Thermo Scientific) results.
Maintained by Ben Bruyneel. Last updated 1 years ago.
mass-spectrometryproteomicsproteomics-data-analysis
3.3 match 2 stars 3.00 score 2 scriptsbioc
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.
biomedicalinformaticssequencingsinglecell
1.7 match 3 stars 5.83 score 15 scripts
r-world-devs
GitStats:Standardized Git Repository Data
Obtain standardized data from multiple 'Git' services, including 'GitHub' and 'GitLab'. Designed to be 'Git' service-agnostic, this package assists teams with activities spread across various 'Git' platforms by providing a unified way to access repository data.
Maintained by Maciej Banas. Last updated 1 months ago.
1.5 match 4 stars 6.51 score 10 scripts 1 dependentscran
gamair:Data for 'GAMs: An Introduction with R'
Data sets and scripts used in the book 'Generalized Additive Models: An Introduction with R', Wood (2006,2017) CRC.
Maintained by Simon Wood. Last updated 6 years ago.
4.0 match 2.43 score 162 scripts
fgazzelloni
hmsidwR:Health Metrics and the Spread of Infectious Diseases
A collection of datasets and supporting functions accompanying Health Metrics and the Spread of Infectious Diseases by Federica Gazzelloni (2024). This package provides data for health metrics calculations, including Disability-Adjusted Life Years (DALYs), Years of Life Lost (YLLs), and Years Lived with Disability (YLDs), as well as additional tools for analyzing and visualizing health data. Federica Gazzelloni (2024) <doi:10.5281/zenodo.10818338>.
Maintained by Federica Gazzelloni. Last updated 2 months ago.
deathshealth-datainfectious-diseaseslifeexpectancy
1.8 match 4 stars 5.48 score 6 scripts
tsiamut
ch:About some Small Functions
The solution to some common problems is proposed, as well as a summary of some small functions. In particular, it provides a useful function for some problems in chemistry. For example, monoa(), monob() and mono() function can be used to calculate The pH of weak acid/base. The ggpng() function can save the PNG format with transparent background. The period_table() function will show the periodic table. Also the show_ruler() function will show the ruler. The show_color() function is funny and easier to show colors. I also provide the symb() function to generate multiple symbols at once. The csv2vcf() function provides an easy method to generate a file. The sym2poly() and sym2coef() function can extract coefficients from polynomials.
Maintained by Hailong Chai. Last updated 3 years ago.
2.3 match 2 stars 4.21 score 41 scripts
maialba3
LipidMS:Lipid Annotation for LC-MS/MS DDA or DIA Data
Lipid annotation in untargeted LC-MS lipidomics based on fragmentation rules. Alcoriza-Balaguer MI, Garcia-Canaveras JC, Lopez A, Conde I, Juan O, Carretero J, Lahoz A (2019) <doi:10.1021/acs.analchem.8b03409>.
Maintained by M Isabel Alcoriza-Balaguer. Last updated 7 months ago.
1.8 match 2 stars 5.33 score 12 scripts 1 dependents
iohprofiler
IOHanalyzer:Data Analysis Part of 'IOHprofiler'
The data analysis module for the Iterative Optimization Heuristics Profiler ('IOHprofiler'). This module provides statistical analysis methods for the benchmark data generated by optimization heuristics, which can be visualized through a web-based interface. The benchmark data is usually generated by the experimentation module, called 'IOHexperimenter'. 'IOHanalyzer' also supports the widely used 'COCO' (Comparing Continuous Optimisers) data format for benchmarking.
Maintained by Diederick Vermetten. Last updated 10 months ago.
1.8 match 24 stars 5.10 score 13 scripts
sere3s
takos:Analysis of Differential Calorimetry Scans
It includes functions for applying methodologies utilized for single-process kinetic analysis of solid-state processes were recently summarized and described in the Recommendation of ICTAC Kinetic Committee. These methods work with the basic kinetic equation. The Methodologies included refers to Avrami, Friedman, Kissinger, Ozawa, OFM, Mo, Starink, isoconversional methodology (Vyazovkin) according to ICATAC Kinetics Committee recommendations as reported in Vyazovkin S, Chrissafis K, Di Lorenzo ML, et al. ICTAC Kinetics Committee recommendations for collecting experimental thermal analysis data for kinetic computations. Thermochim Acta. 2014; 590:1-23. <doi:10.1016/J.TCA.2014.05.036> .
Maintained by Serena Berretta. Last updated 4 years ago.
3.1 match 4 stars 2.92 score 21 scripts
wilarhen
measuRing:Detection and Control of Tree-Ring Widths on Scanned Image Sections
Identification of ring borders on scanned image sections from dendrochronological samples. Processing of image reflectances to produce gray matrices and time series of smoothed gray values. Luminance data is plotted on segmented images for users to perform both: visual identification of ring borders or control of automatic detection. Routines to visually include/exclude ring borders on the R graphical devices, or automatically detect ring borders using a linear detection algorithm. This algorithm detects ring borders according to positive/negative extreme values in the smoothed time-series of gray values. Most of the in-package routines can be recursively implemented using the multiDetect() function.
Maintained by Wilson Lara. Last updated 7 years ago.
5.0 match 1.80 score 21 scripts 1 dependentsbioc
MethReg:Assessing the regulatory potential of DNA methylation regions or sites on gene transcription
Epigenome-wide association studies (EWAS) detects a large number of DNA methylation differences, often hundreds of differentially methylated regions and thousands of CpGs, that are significantly associated with a disease, many are located in non-coding regions. Therefore, there is a critical need to better understand the functional impact of these CpG methylations and to further prioritize the significant changes. MethReg is an R package for integrative modeling of DNA methylation, target gene expression and transcription factor binding sites data, to systematically identify and rank functional CpG methylations. MethReg evaluates, prioritizes and annotates CpG sites with high regulatory potential using matched methylation and gene expression data, along with external TF-target interaction databases based on manually curation, ChIP-seq experiments or gene regulatory network analysis.
Maintained by Tiago Silva. Last updated 5 months ago.
methylationarrayregressiongeneexpressionepigeneticsgenetargettranscription
1.6 match 5 stars 5.45 score 19 scripts
biometris
statgenMPP:QTL Mapping for Multi Parent Populations
For Multi Parent Populations (MPP) Identity By Descend (IBD) probabilities are computed using Hidden Markov Models. These probabilities are then used in a mixed model approach for QTL Mapping as described in Li et al. (<doi:10.1007/s00122-021-03919-7>).
Maintained by Bart-Jan van Rossum. Last updated 1 months ago.
1.8 match 4.94 score 11 scriptsbioc
methimpute:Imputation-guided re-construction of complete methylomes from WGBS data
This package implements functions for calling methylation for all cytosines in the genome.
Maintained by Aaron Taudt. Last updated 5 months ago.
immunooncologysoftwarednamethylationepigeneticshiddenmarkovmodelsequencingcoveragecppopenmp
2.0 match 4.11 score 13 scriptsbioc
CardinalIO:Read and write mass spectrometry imaging files
Fast and efficient reading and writing of mass spectrometry imaging data files. Supports imzML and Analyze 7.5 formats. Provides ontologies for mass spectrometry imaging.
Maintained by Kylie Ariel Bemis. Last updated 5 months ago.
softwareinfrastructuredataimportmassspectrometryimagingmassspectrometrycpp
1.5 match 1 stars 5.35 score 3 scripts 1 dependents
glotaran
TIMP:Fitting Separable Nonlinear Models in Spectroscopy and Microscopy
A problem solving environment (PSE) for fitting separable nonlinear models to measurements arising in physics and chemistry experiments, as described by Mullen & van Stokkum (2007) <doi:10.18637/jss.v018.i03> for its use in fitting time resolved spectroscopy data, and as described by Laptenok et al. (2007) <doi:10.18637/jss.v018.i08> for its use in fitting Fluorescence Lifetime Imaging Microscopy (FLIM) data, in the study of Förster Resonance Energy Transfer (FRET). `TIMP` also serves as the computation backend for the `GloTarAn` software, a graphical user interface for the package, as described in Snellenburg et al. (2012) <doi:10.18637/jss.v049.i03>.
Maintained by Joris Snellenburg. Last updated 2 years ago.
1.7 match 3 stars 4.80 score 14 scripts 1 dependents
gorelab
waves:Vis-NIR Spectral Analysis Wrapper
Originally designed application in the context of resource-limited plant research and breeding programs, 'waves' provides an open-source solution to spectral data processing and model development by bringing useful packages together into a streamlined pipeline. This package is wrapper for functions related to the analysis of point visible and near-infrared reflectance measurements. It includes visualization, filtering, aggregation, preprocessing, cross-validation set formation, model training, and prediction functions to enable open-source association of spectral and reference data. This package is documented in a peer-reviewed manuscript in the Plant Phenome Journal <doi:10.1002/ppj2.20012>. Specialized cross-validation schemes are described in detail in Jarquín et al. (2017) <doi:10.3835/plantgenome2016.12.0130>. Example data is from Ikeogu et al. (2017) <doi:10.1371/journal.pone.0188918>.
Maintained by Jenna Hershberger. Last updated 11 months ago.
1.3 match 6 stars 5.98 score 53 scripts
apwheele
ptools:Tools for Poisson Data
Functions used for analyzing count data, mostly crime counts. Includes checking difference in two Poisson counts (e-test), checking the fit for a Poisson distribution, small sample tests for counts in bins, Weighted Displacement Difference test (Wheeler and Ratcliffe, 2018) <doi:10.1186/s40163-018-0085-5>, to evaluate crime changes over time in treated/control areas. Additionally includes functions for aggregating spatial data and spatial feature engineering.
Maintained by Andrew Wheeler. Last updated 1 years ago.
crime-analysiscriminal-justicecriminology
1.8 match 5 stars 4.44 score 11 scriptsbioc
TVTB:TVTB: The VCF Tool Box
The package provides S4 classes and methods to filter, summarise and visualise genetic variation data stored in VCF files. In particular, the package extends the FilterRules class (S4Vectors package) to define news classes of filter rules applicable to the various slots of VCF objects. Functionalities are integrated and demonstrated in a Shiny web-application, the Shiny Variant Explorer (tSVE).
Maintained by Kevin Rue-Albrecht. Last updated 5 months ago.
softwaregeneticsgeneticvariabilitygenomicvariationdatarepresentationguidnaseqwholegenomevisualizationmultiplecomparisondataimportvariantannotationsequencingcoveragealignmentsequencematching
1.3 match 2 stars 5.76 score 16 scripts
jimb3
GxEScanR:Run GWAS/GWEIS Scans Using Binary Dosage Files
Tools to run genome-wide association study (GWAS) and genome-wide by environment interaction study (GWEIS) scans using the genetic data stored in a binary dosage file. The user provides a data frame with the subject's covariate data and the information about the binary dosage file returned by the BinaryDosage::getbdinfo() routine.
Maintained by John Morrison. Last updated 4 years ago.
3.3 match 2.28 score 19 scriptsbioc
GeneRegionScan:GeneRegionScan
A package with focus on analysis of discrete regions of the genome. This package is useful for investigation of one or a few genes using Affymetrix data, since it will extract probe level data using the Affymetrix Power Tools application and wrap these data into a ProbeLevelSet. A ProbeLevelSet directly extends the expressionSet, but includes additional information about the sequence of each probe and the probe set it is derived from. The package includes a number of functions used for plotting these probe level data as a function of location along sequences of mRNA-strands. This can be used for analysis of variable splicing, and is especially well suited for use with exon-array data.
Maintained by Lasse Folkersen. Last updated 5 months ago.
microarraydataimportsnponechannelvisualization
2.0 match 3.78 score 1 scriptsbioc
cosmiq:cosmiq - COmbining Single Masses Into Quantities
cosmiq is a tool for the preprocessing of liquid- or gas - chromatography mass spectrometry (LCMS/GCMS) data with a focus on metabolomics or lipidomics applications. To improve the detection of low abundant signals, cosmiq generates master maps of the mZ/RT space from all acquired runs before a peak detection algorithm is applied. The result is a more robust identification and quantification of low-intensity MS signals compared to conventional approaches where peak picking is performed in each LCMS/GCMS file separately. The cosmiq package builds on the xcmsSet object structure and can be therefore integrated well with the package xcms as an alternative preprocessing step.
Maintained by David Fischer. Last updated 5 months ago.
immunooncologymassspectrometrymetabolomics
1.7 match 4.48 score 2 scriptsrqtl
qtl2fst:Database Storage of Genotype Probabilities for QTL Mapping
Uses the 'fst' package to store genotype probabilities on disk for the 'qtl2' package. These genotype probabilities are a central data object for mapping quantitative trait loci (QTL), but they can be quite large. The facilities in this package enable the genotype probabilities to be stored on disk, leading to reduced memory usage with only a modest increase in computation time.
Maintained by Karl W Broman. Last updated 4 months ago.
1.5 match 2 stars 4.95 score 15 scripts 1 dependents
bayesstats
bamdit:Bayesian Meta-Analysis of Diagnostic Test Data
Provides a new class of Bayesian meta-analysis models that incorporates a model for internal and external validity bias. In this way, it is possible to combine studies of diverse quality and different types. For example, we can combine the results of randomized control trials (RCTs) with the results of observational studies (OS).
Maintained by Pablo Emilio Verde. Last updated 1 months ago.
3.6 match 2.05 score 14 scriptsbioc
LOBSTAHS:Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences
LOBSTAHS is a multifunction package for screening, annotation, and putative identification of mass spectral features in large, HPLC-MS lipid datasets. In silico data for a wide range of lipids, oxidized lipids, and oxylipins can be generated from user-supplied structural criteria with a database generation function. LOBSTAHS then applies these databases to assign putative compound identities to features in any high-mass accuracy dataset that has been processed using xcms and CAMERA. Users can then apply a series of orthogonal screening criteria based on adduct ion formation patterns, chromatographic retention time, and other properties, to evaluate and assign confidence scores to this list of preliminary assignments. During the screening routine, LOBSTAHS rejects assignments that do not meet the specified criteria, identifies potential isomers and isobars, and assigns a variety of annotation codes to assist the user in evaluating the accuracy of each assignment.
Maintained by Henry Holm. Last updated 5 months ago.
immunooncologymassspectrometrymetabolomicslipidomicsdataimportadductalgaebioconductorhplc-esi-mslipidmass-spectrometryoxidative-stress-biomarkersoxidized-lipidsoxylipinsplankton
1.1 match 8 stars 6.56 score 9 scripts
jmmonnet
lidaRtRee:Forest Analysis with Airborne Laser Scanning (LiDAR) Data
Provides functions for forest objects detection, structure metrics computation, model calibration and mapping with airborne laser scanning: co-registration of field plots (Monnet and Mermin (2014) <doi:10.3390/f5092307>); tree detection (method 1 in Eysn et al. (2015) <doi:10.3390/f6051721>) and segmentation; forest parameters estimation with the area-based approach: model calibration with ground reference, and maps export (Aussenac et al. (2023) <doi:10.12688/openreseurope.15373.2>); extraction of both physical (gaps, edges, trees) and statistical features useful for e.g. habitat suitability modeling (Glad et al. (2020) <doi:10.1002/rse2.117>) and forest maturity mapping (Fuhr et al. (2022) <doi:10.1002/rse2.274>).
Maintained by Jean-Matthieu Monnet. Last updated 2 months ago.
3.4 match 3 stars 2.18 score
yufree
enviGCMS:GC/LC-MS Data Analysis for Environmental Science
Gas/Liquid Chromatography-Mass Spectrometer(GC/LC-MS) Data Analysis for Environmental Science. This package covered topics such molecular isotope ratio, matrix effects and Short-Chain Chlorinated Paraffins analysis etc. in environmental analysis.
Maintained by Miao YU. Last updated 2 months ago.
environmentmass-spectrometrymetabolomics
1.1 match 17 stars 6.49 score 30 scripts 1 dependentsbioc
PAA:PAA (Protein Array Analyzer)
PAA imports single color (protein) microarray data that has been saved in gpr file format - esp. ProtoArray data. After preprocessing (background correction, batch filtering, normalization) univariate feature preselection is performed (e.g., using the "minimum M statistic" approach - hereinafter referred to as "mMs"). Subsequently, a multivariate feature selection is conducted to discover biomarker candidates. Therefore, either a frequency-based backwards elimination aproach or ensemble feature selection can be used. PAA provides a complete toolbox of analysis tools including several different plots for results examination and evaluation.
Maintained by Michael Turewicz. Last updated 5 months ago.
classificationmicroarrayonechannelproteomicscpp
1.7 match 4.34 score 11 scriptsbioc
adductomicsR:Processing of adductomic mass spectral datasets
Processes MS2 data to identify potentially adducted peptides from spectra that has been corrected for mass drift and retention time drift and quantifies MS1 level mass spectral peaks.
Maintained by Josie Hayes. Last updated 5 months ago.
massspectrometrymetabolomicssoftwarethirdpartyclientdataimportgui
1.8 match 1 stars 4.00 score 5 scripts
fishioka
echelon:The Echelon Analysis and the Detection of Spatial Clusters using Echelon Scan Method
Functions for the echelon analysis proposed by Myers et al. (1997) <doi:10.1023/A:1018518327329>, and the detection of spatial clusters using echelon scan method proposed by Kurihara (2003) <doi:10.20551/jscswabun.15.2_171>.
Maintained by Fumio Ishioka. Last updated 13 days ago.
6.7 match 1.00 score
kopflab
lans2r:Work with Look at NanoSIMS Data in R
R interface for working with nanometer scale secondary ion mass spectrometry (NanoSIMS) data exported from Look at NanoSIMS.
Maintained by Sebastian Kopf. Last updated 2 years ago.
geobiologygeochemistryisotopesnanosims
1.5 match 4.32 score 14 scripts
zpneal
grand:Guidelines for Reporting About Network Data
Interactively applies the Guidelines for Reporting About Network Data (GRAND) to an 'igraph' object, and generates a uniform narrative or tabular description of the object.
Maintained by Zachary Neal. Last updated 2 years ago.
1.8 match 1 stars 3.70 score 2 scripts
mrcieu
CAMeRa:CAMeRa (Cross Ancestral Mendelian Randomisation)
CAMERA estimates joint causal effect in multiple ancestries and detects pleiotropy via the zero relevance model.
Maintained by Gibran Hemani. Last updated 12 months ago.
causal-inferencegwas-summary-statisticsmendelian-randomisationmulti-ancestry
1.1 match 2 stars 5.32 score 175 scriptsbioc
FindIT2:find influential TF and Target based on multi-omics data
This package implements functions to find influential TF and target based on different input type. It have five module: Multi-peak multi-gene annotaion(mmPeakAnno module), Calculate regulation potential(calcRP module), Find influential Target based on ChIP-Seq and RNA-Seq data(Find influential Target module), Find influential TF based on different input(Find influential TF module), Calculate peak-gene or peak-peak correlation(peakGeneCor module). And there are also some other useful function like integrate different source information, calculate jaccard similarity for your TF.
Maintained by Guandong Shang. Last updated 5 months ago.
softwareannotationchipseqatacseqgeneregulationmultiplecomparisongenetarget
1.1 match 6 stars 5.26 score 7 scripts
henrikbengtsson
port4me:Get the Same, Personal, Free 'TCP' Port over and over
An R implementation of the cross-platform, language-independent "port4me" algorithm (<https://github.com/HenrikBengtsson/port4me>), which (1) finds a free Transmission Control Protocol ('TCP') port in [1024,65535] that the user can open, (2) is designed to work in multi-user environments, (3), gives different users, different ports, (4) gives the user the same port over time with high probability, (5) gives different ports for different software tools, and (6) requires no configuration.
Maintained by Henrik Bengtsson. Last updated 1 years ago.
bashclihigh-performance-computinghpcmulti-tenantmulti-userportpypi-packagepythonr-languager-programmingtcputility
1.1 match 13 stars 5.11 score 5 scripts
boxuancui
DataExplorer:Automate Data Exploration and Treatment
Automated data exploration process for analytic tasks and predictive modeling, so that users could focus on understanding data and extracting insights. The package scans and analyzes each variable, and visualizes them with typical graphical techniques. Common data processing methods are also available to treat and format data.
Maintained by Boxuan Cui. Last updated 1 years ago.
data-analysisdata-explorationdata-scienceedavisualization
0.5 match 519 stars 11.16 score 2.2k scripts
michelenuijten
statcheck:Extract Statistics from Articles and Recompute P-Values
A "spellchecker" for statistics. It checks whether your p-values match their accompanying test statistic and degrees of freedom. statcheck searches for null-hypothesis significance test (NHST) in APA style (e.g., t(28) = 2.2, p < .05). It recalculates the p-value using the reported test statistic and degrees of freedom. If the reported and computed p-values don't match, statcheck will flag the result as an error. If the reported p-value is statistically significant and the recomputed one is not, or vice versa, the result will be flagged as a decision error. You can use statcheck directly on a string of text, but you can also scan a PDF or HTML file, or even a folder of PDF and/or HTML files. Statcheck needs an external program to convert PDF to text: Xpdf. Instructions on where and how to download this program, how to install statcheck, and more details on what statcheck can and cannot do can be found in the online manual: <https://rpubs.com/michelenuijten/statcheckmanual>. You can find a point-and-click web interface to scan PDF or HTML or DOCX articles on <http://statcheck.io>.
Maintained by Michele B. Nuijten. Last updated 8 months ago.
nhstp-valuesreproducibilitystatistics
0.8 match 175 stars 7.54 score 40 scripts
ishidamgm
TreeRingShape:Recording Tree-Ring Shapes of Tree Disks with Manual Digitizing and Interpolating Model
Record all tree-ring Shapefile of tree disk with GIS soft ('Qgis'<https://www.qgis.org/en/site/>) and interpolating model from high resolution tree disk image.
Maintained by Megumi ISHIDA. Last updated 4 months ago.
1.2 match 4.48 score
hypertidy
fasterize:Fast Polygon to Raster Conversion
Provides a drop-in replacement for rasterize() from the 'raster' package that takes polygon vector or data frame objects, and is much faster. There is support for the main options provided by the rasterize() function, including setting the field used and background value, and options for aggregating multi-layer rasters. Uses the scan line algorithm attributed to Wylie et al. (1967) <doi:10.1145/1465611.1465619>. Note that repository originally was hosted at 'Github' 'ecohealthalliance/fasterize' but was migrated to 'hypertidy/fasterize' in March 2025, and can be found indexed on 'R universe' <https://cran.r-universe.dev/fasterize>.
Maintained by Michael Sumner. Last updated 8 days ago.
rasterrcpprcpparmadillosfspatialcpp
0.5 match 182 stars 10.05 score 14 dependents
sens
qtlDesign:Design of QTL (Quantitative Trait Locus) Experiments
Design of QTL (quantitative trait locus) experiments involves choosing which strains to cross, the type of cross, genotyping strategies, phenotyping strategies, and the number of progeny to raise and phenotype. This package provides tools to help make such choices. Sen and others (2007) <doi:10.1007/s00335-006-0090-y>.
Maintained by Saunak Sen. Last updated 11 months ago.
1.8 match 1 stars 2.90 score 32 scripts
lcbc-uio
noasr:NOAS convenience functions
Functions created to work well with LCBC's Nephew of All Spreadsheet data.
Maintained by Athanasia Mo Mowinckel. Last updated 4 years ago.
1.7 match 3.00 score 4 scriptscsafe-isu
handwriter:Handwriting Analysis in R
Perform statistical writership analysis of scanned handwritten documents. Webpage provided at: <https://github.com/CSAFE-ISU/handwriter>.
Maintained by Stephanie Reinders. Last updated 1 months ago.
0.5 match 24 stars 8.70 score 27 scripts 2 dependentsspatstat
spatstat.model:Parametric Statistical Modelling and Inference for the 'spatstat' Family
Functionality for parametric statistical modelling and inference for spatial data, mainly spatial point patterns, in the 'spatstat' family of packages. (Excludes analysis of spatial data on a linear network, which is covered by the separate package 'spatstat.linnet'.) Supports parametric modelling, formal statistical inference, and model validation. Parametric models include Poisson point processes, Cox point processes, Neyman-Scott cluster processes, Gibbs point processes and determinantal point processes. Models can be fitted to data using maximum likelihood, maximum pseudolikelihood, maximum composite likelihood and the method of minimum contrast. Fitted models can be simulated and predicted. Formal inference includes hypothesis tests (quadrat counting tests, Cressie-Read tests, Clark-Evans test, Berman test, Diggle-Cressie-Loosmore-Ford test, scan test, studentised permutation test, segregation test, ANOVA tests of fitted models, adjusted composite likelihood ratio test, envelope tests, Dao-Genton test, balanced independent two-stage test), confidence intervals for parameters, and prediction intervals for point counts. Model validation techniques include leverage, influence, partial residuals, added variable plots, diagnostic plots, pseudoscore residual plots, model compensators and Q-Q plots.
Maintained by Adrian Baddeley. Last updated 8 days ago.
analysis-of-variancecluster-processconfidence-intervalscox-processdeterminantal-point-processesgibbs-processinfluenceleveragemodel-diagnosticsneyman-scottparameter-estimationpoisson-processspatial-analysisspatial-modellingspatial-point-processesstatistical-inference
0.5 match 5 stars 9.09 score 6 scripts 46 dependentscran
jmuOutlier:Permutation Tests for Nonparametric Statistics
Performs a permutation test on the difference between two location parameters, a permutation correlation test, a permutation F-test, the Siegel-Tukey test, a ratio mean deviance test. Also performs some graphing techniques, such as for confidence intervals, vector addition, and Fourier analysis; and includes functions related to the Laplace (double exponential) and triangular distributions. Performs power calculations for the binomial test.
Maintained by Steven T. Garren. Last updated 6 years ago.
1.9 match 2.26 score 1 dependents
dfsp-spirit
freesurferformats:Read and Write 'FreeSurfer' Neuroimaging File Formats
Provides functions to read and write neuroimaging data in various file formats, with a focus on 'FreeSurfer' <http://freesurfer.net/> formats. This includes, but is not limited to, the following file formats: 1) MGH/MGZ format files, which can contain multi-dimensional images or other data. Typically they contain time-series of three-dimensional brain scans acquired by magnetic resonance imaging (MRI). They can also contain vertex-wise measures of surface morphometry data. The MGH format is named after the Massachusetts General Hospital, and the MGZ format is a compressed version of the same format. 2) 'FreeSurfer' morphometry data files in binary 'curv' format. These contain vertex-wise surface measures, i.e., one scalar value for each vertex of a brain surface mesh. These are typically values like the cortical thickness or brain surface area at each vertex. 3) Annotation file format. This contains a brain surface parcellation derived from a cortical atlas. 4) Surface file format. Contains a brain surface mesh, given by a list of vertices and a list of faces.
Maintained by Tim Schäfer. Last updated 6 months ago.
brainbrain-atlasbrain-surfacescurvdtifileformatsfreesurferlabelmeshmghmrineuroimagingparcellationresearchsurfacevoxel
0.5 match 23 stars 8.07 score 25 scripts 8 dependents
bristol-vaccine-centre
avoncap:AvonCap Study Analysis
A WIP set of functions allowing data load, wrangling of the AvonCap data set.
Maintained by Rob Challen. Last updated 3 months ago.
1.7 match 2.34 score 11 scripts
kwb-r
fakin.path.app:Shiny App to Visualise File Paths
This package contains an R Shiny App that loads file path information from a file and displays the paths in different ways. The aim of the app is to find weaknesses in the folder structure.
Maintained by Hauke Sonnenberg. Last updated 4 years ago.
path-analysisproject-fakinshiny-app
1.2 match 3.18 score 1 scripts 1 dependents
tgoodbody
sgsR:Structurally Guided Sampling
Structurally guided sampling (SGS) approaches for airborne laser scanning (ALS; LIDAR). Primary functions provide means to generate data-driven stratifications & methods for allocating samples. Intermediate functions for calculating and extracting important information about input covariates and samples are also included. Processing outcomes are intended to help forest and environmental management practitioners better optimize field sample placement as well as assess and augment existing sample networks in the context of data distributions and conditions. ALS data is the primary intended use case, however any rasterized remote sensing data can be used, enabling data-driven stratifications and sampling approaches.
Maintained by Tristan RH Goodbody. Last updated 14 days ago.
0.5 match 46 stars 7.50 score 34 scriptscran
R4HCR:R for Health Care Research
A collection of datasets that accompany the forthcoming book "R for Health Care Research".
Maintained by Jason L. Oke. Last updated 6 months ago.
3.8 match 1.00 scorecran
rNeighborQTL:Interval Mapping for Quantitative Trait Loci Underlying Neighbor Effects
To enable quantitative trait loci mapping of neighbor effects, this package extends a single-marker regression to interval mapping. The theoretical background of the method is described in Sato et al. (2021) <doi:10.1093/g3journal/jkab017>.
Maintained by Yasuhiro Sato. Last updated 4 years ago.
1.8 match 2.00 score 3 scriptsbioc
dmrseq:Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing
This package implements an approach for scanning the genome to detect and perform accurate inference on differentially methylated regions from Whole Genome Bisulfite Sequencing data. The method is based on comparing detected regions to a pooled null distribution, that can be implemented even when as few as two samples per population are available. Region-level statistics are obtained by fitting a generalized least squares (GLS) regression model with a nested autoregressive correlated error structure for the effect of interest on transformed methylation proportions.
Maintained by Keegan Korthauer. Last updated 5 months ago.
immunooncologydnamethylationepigeneticsmultiplecomparisonsoftwaresequencingdifferentialmethylationwholegenomeregressionfunctionalgenomics
0.5 match 6.39 score 59 scripts 1 dependentscsafe-isu
handwriterRF:Handwriting Analysis with Random Forests
Perform forensic handwriting analysis of two scanned handwritten documents. This package implements the statistical method described by Madeline Johnson and Danica Ommen (2021) <doi:10.1002/sam.11566>. Similarity measures and a random forest produce a score-based likelihood ratio that quantifies the strength of the evidence in favor of the documents being written by the same writer or different writers.
Maintained by Stephanie Reinders. Last updated 9 days ago.
0.5 match 2 stars 6.18 score 15 scripts 1 dependentsbioc
martini:GWAS Incorporating Networks
martini deals with the low power inherent to GWAS studies by using prior knowledge represented as a network. SNPs are the vertices of the network, and the edges represent biological relationships between them (genomic adjacency, belonging to the same gene, physical interaction between protein products). The network is scanned using SConES, which looks for groups of SNPs maximally associated with the phenotype, that form a close subnetwork.
Maintained by Hector Climente-Gonzalez. Last updated 5 months ago.
softwaregenomewideassociationsnpgeneticvariabilitygeneticsfeatureextractiongraphandnetworknetworkbioinformaticsgenomicsgwasnetwork-analysissnpssystems-biologycpp
0.5 match 4 stars 6.16 score 30 scripts
draalmeida
leafR:Calculates the Leaf Area Index (LAD) and Other Related Functions
A set of functions for analyzing the structure of forests based on the leaf area density (LAD) and leaf area index (LAI) measures calculated from Airborne Laser Scanning (ALS), i.e., scanning lidar (Light Detection and Ranging) data. The methodology is discussed and described in Almeida et al. (2019) <doi:10.3390/rs11010092> and Stark et al. (2012) <doi:10.1111/j.1461-0248.2012.01864.x>.
Maintained by Danilo Roberti Alves de Almeida. Last updated 4 years ago.
0.8 match 17 stars 3.93 score 4 scripts
skranz
rmdtools:Tools for RMarkdown
Tools for RMarkdown
Maintained by Sebastian Kranz. Last updated 4 years ago.
1.7 match 1 stars 1.78 score 6 scripts 2 dependents
elliottsmeds
lacunr:Fast 3D Lacunarity for Voxel Data
Calculates 3D lacunarity from voxel data. It is designed for use with point clouds generated from Light Detection And Ranging (LiDAR) scans in order to measure the spatial heterogeneity of 3-dimensional structures such as forest stands. It provides fast 'C++' functions to efficiently bin point cloud data into voxels and calculate lacunarity using different variants of the gliding-box algorithm originated by Allain & Cloitre (1991) <doi:10.1103/PhysRevA.44.3552>.
Maintained by Elliott Smeds. Last updated 9 months ago.
0.5 match 4 stars 5.56 score 7 scriptshypertidy
ncdump:Extract Metadata from 'NetCDF' Files as Data Frames
Tools for handling 'NetCDF' metadata in data frames. The metadata is provided as relations in tabular form, to avoid having to scan printed header output or to navigate nested lists of raw metadata.
Maintained by Michael D. Sumner. Last updated 1 months ago.
0.5 match 3 stars 5.36 score 38 scripts