R-universe search: name

ropensci

taxize:Taxonomic Information from Around the Web

Interacts with a suite of web application programming interfaces (API) for taxonomic tasks, such as getting database specific taxonomic identifiers, verifying species names, getting taxonomic hierarchies, fetching downstream and upstream taxonomic names, getting taxonomic synonyms, converting scientific to common names and vice versa, and more. Some of the services supported include 'NCBI E-utilities' (<https://www.ncbi.nlm.nih.gov/books/NBK25501/>), 'Encyclopedia of Life' (<https://eol.org/docs/what-is-eol/data-services>), 'Global Biodiversity Information Facility' (<https://techdocs.gbif.org/en/openapi/>), and many more. Links to the API documentation for other supported services are available in the documentation for their respective functions in this package.

Maintained by Zachary Foster. Last updated 12 days ago.

taxonomy biology nomenclature json api web api-client identifiers species names api-wrapper biodiversity darwincore data taxize

143.4 match 274 stars 13.63 score 1.6k scripts 23 dependents

easystats

insight:Easy Access to Model Information for Various Model Objects

A tool to provide an easy, intuitive and consistent access to information contained in various R models, like model formulas, model terms, information about random effects, data that was used to fit the model or data from response variables. 'insight' mainly revolves around two types of functions: Functions that find (the names of) information, starting with 'find_', and functions that get the underlying data, starting with 'get_'. The package has a consistent syntax and works with many different model objects, where otherwise functions to access these information are missing.

Maintained by Daniel Lüdecke. Last updated 5 days ago.

easystats hacktoberfest insight models names predictors random

43.4 match 412 stars 17.24 score 568 scripts 210 dependents

miraisolutions

XLConnect:Excel Connector for R

Provides comprehensive functionality to read, write and format Excel data.

Maintained by Martin Studer. Last updated 17 days ago.

cross-platform excel r-language xlconnect openjdk

43.1 match 130 stars 12.28 score 1.2k scripts 1 dependents

matthewheun

matsbyname:An Implementation of Matrix Mathematics that Respects Row and Column Names

An implementation of matrix mathematics wherein operations are performed "by name."

Maintained by Matthew Heun. Last updated 10 days ago.

74.2 match 2 stars 6.65 score 150 scripts 1 dependents

bioc

ComplexHeatmap:Make Complex Heatmaps

Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports various annotation graphics.

Maintained by Zuguang Gu. Last updated 5 months ago.

software visualization sequencing clustering complex-heatmaps heatmap

28.0 match 1.3k stars 16.93 score 16k scripts 151 dependents

dankelley

oce:Analysis of Oceanographic Data

Supports the analysis of Oceanographic data, including 'ADCP' measurements, measurements made with 'argo' floats, 'CTD' measurements, sectional data, sea-level time series, coastline and topographic data, etc. Provides specialized functions for calculating seawater properties such as potential temperature in either the 'UNESCO' or 'TEOS-10' equation of state. Produces graphical displays that conform to the conventions of the Oceanographic literature. This package is discussed extensively by Kelley (2018) "Oceanographic Analysis with R" <doi:10.1007/978-1-4939-8844-0>.

Maintained by Dan Kelley. Last updated 1 days ago.

oceanography fortran cpp

30.7 match 146 stars 15.42 score 4.2k scripts 18 dependents

ropensci

beautier:'BEAUti' from R

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

Maintained by Richèl J.C. Bilderbeek. Last updated 22 days ago.

bayesian beast beast2 beauti phylogenetic-inference phylogenetics

46.6 match 13 stars 8.76 score 198 scripts 5 dependents

winvector

wrapr:Wrap R Tools for Debugging and Parametric Programming

Tools for writing and debugging R code. Provides: '%.>%' dot-pipe (an 'S3' configurable pipe), unpack/to (R style multiple assignment/return), 'build_frame()'/'draw_frame()' ('data.frame' example tools), 'qc()' (quoting concatenate), ':=' (named map builder), 'let()' (converts non-standard evaluation interfaces to parametric standard evaluation interfaces, inspired by 'gtools::strmacro()' and 'base::bquote()'), and more.

Maintained by John Mount. Last updated 2 years ago.

36.4 match 137 stars 11.11 score 390 scripts 12 dependents

r-lib

rlang:Functions for Base Types and Core R and 'Tidyverse' Features

A toolbox for working with base types, core R features like the condition system, and core 'Tidyverse' features like tidy evaluation.

Maintained by Lionel Henry. Last updated 19 days ago.

19.2 match 517 stars 20.53 score 9.8k scripts 15k dependents

christopherkenny

name:Tools for Working with Names

A system for organizing column names in data. Aimed at supporting a prefix-based and suffix-based column naming scheme. Extends 'dplyr' functionality to add ordering by function and more explicit renaming.

Maintained by Christopher T. Kenny. Last updated 3 years ago.

61.0 match 2 stars 6.28 score 19k scripts

tiledb-inc

tiledb:Modern Database Engine for Complex Data Based on Multi-Dimensional Arrays

The modern database 'TileDB' introduces a powerful on-disk format for storing and accessing any complex data based on multi-dimensional arrays. It supports dense and sparse arrays, dataframes and key-values stores, cloud storage ('S3', 'GCS', 'Azure'), chunked arrays, multiple compression, encryption and checksum filters, uses a fully multi-threaded implementation, supports parallel I/O, data versioning ('time travel'), metadata and groups. It is implemented as an embeddable cross-platform C++ library with APIs from several languages, and integrations. This package provides the R support.

Maintained by Isaiah Norton. Last updated 4 days ago.

array hdfs s3 storage-manager tiledb cpp

31.7 match 107 stars 11.96 score 306 scripts 4 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 3 days ago.

arrow polars rust

30.1 match 499 stars 12.01 score 1.0k scripts 2 dependents

crlsierra

SoilR:Models of Soil Organic Matter Decomposition

Functions for modeling Soil Organic Matter decomposition in terrestrial ecosystems with linear and nonlinear systems of differential equations. The package implements models according to the compartmental system representation described in Sierra and others (2012) <doi:10.5194/gmd-5-1045-2012> and Sierra and others (2014) <doi:10.5194/gmd-7-1919-2014>.

Maintained by Carlos A. Sierra. Last updated 1 years ago.

115.4 match 5 stars 2.88 score 153 scripts

trevorld

gridpattern:'grid' Pattern Grobs

Provides 'grid' grobs that fill in a user-defined area with various patterns. Includes enhanced versions of the geometric and image-based patterns originally contained in the 'ggpattern' package as well as original 'pch', 'polygon_tiling', 'regular_polygon', 'rose', 'text', 'wave', and 'weave' patterns plus support for custom user-defined patterns.

Maintained by Trevor L. Davis. Last updated 1 months ago.

39.0 match 33 stars 8.42 score 4 scripts 4 dependents

ncss-tech

aqp:Algorithms for Quantitative Pedology

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

Maintained by Dylan Beaudette. Last updated 29 days ago.

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

27.2 match 55 stars 11.77 score 1.2k scripts 2 dependents

bioc

phyloseq:Handling and analysis of high-throughput microbiome census data

phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.

Maintained by Paul J. McMurdie. Last updated 5 months ago.

immunooncology sequencing microbiome metagenomics clustering classification multiplecomparison geneticvariability

21.4 match 597 stars 13.90 score 8.4k scripts 37 dependents

psychbruce

ChineseNames:Chinese Name Database 1930-2008

A database of Chinese surnames and Chinese given names (1930-2008). This database contains nationwide frequency statistics of 1,806 Chinese surnames and 2,614 Chinese characters used in given names, covering about 1.2 billion Han Chinese population (96.8% of the Han Chinese household-registered population born from 1930 to 2008 and still alive in 2008). This package also contains a function for computing multiple features of Chinese surnames and Chinese given names for scientific research (e.g., name uniqueness, name gender, name valence, and name warmth/competence).

Maintained by Han-Wu-Shuang Bao. Last updated 1 years ago.

big-data chinese chinese-name chinese-names database name names

60.7 match 147 stars 4.87 score 6 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 days ago.

12.5 match 3.7k stars 23.53 score 230k scripts 4.6k dependents

chengvt

EEM:Read and Preprocess Fluorescence Excitation-Emission Matrix (EEM) Data

Read raw EEM data and prepares them for further analysis.

Maintained by Vipavee Trivittayasil. Last updated 8 years ago.

42.8 match 8 stars 6.72 score 66 scripts

kwb-r

kwb.utils:General Utility Functions Developed at KWB

This package contains some small helper functions that aim at improving the quality of code developed at Kompetenzzentrum Wasser gGmbH (KWB).

Maintained by Hauke Sonnenberg. Last updated 12 months ago.

38.3 match 8 stars 7.33 score 12 scripts 78 dependents

emilhvitfeldt

paletteer:Comprehensive Collection of Color Palettes

The choices of color palettes in R can be quite overwhelming with palettes spread over many packages with many different API's. This packages aims to collect all color palettes across the R ecosystem under the same package with a streamlined API.

Maintained by Emil Hvitfeldt. Last updated 9 months ago.

color-palette palettes

20.5 match 957 stars 13.50 score 6.9k scripts 23 dependents

ironholds

humaniformat:A Parser for Human Names

Human names are complicated and nonstandard things. Humaniformat, which is based on Anthony Ettinger's 'humanparser' project <https://github.com/chovy/humanparser> provides functions for parsing human names, making a best-guess attempt to distinguish sub-components such as prefixes, suffixes, middle names and salutations.

Maintained by Oliver Keyes. Last updated 8 years ago.

names parser cpp

36.9 match 55 stars 7.42 score 44 scripts 7 dependents

ropensci

rgbif:Interface to the Global Biodiversity Information Facility API

A programmatic interface to the Web Service methods provided by the Global Biodiversity Information Facility (GBIF; <https://www.gbif.org/developer/summary>). GBIF is a database of species occurrence records from sources all over the globe. rgbif includes functions for searching for taxonomic names, retrieving information on data providers, getting species occurrence records, getting counts of occurrence records, and using the GBIF tile map service to make rasters summarizing huge amounts of data.

Maintained by John Waller. Last updated 3 days ago.

gbif specimens api web-services occurrences species taxonomy biodiversity data lifewatch oscibio spocc

20.5 match 161 stars 13.26 score 2.1k scripts 20 dependents

great-northern-diver

loon:Interactive Statistical Data Visualization

An extendable toolkit for interactive data visualization and exploration.

Maintained by R. Wayne Oldford. Last updated 2 years ago.

data-analysis data-science data-visualization exploratory-analysis exploratory-data-analysis high-dimensional-data interactive-graphics interactive-visualizations loon python statistical-analysis statistical-graphics statistics tcl-extension tk

29.8 match 48 stars 9.00 score 93 scripts 5 dependents

ycphs

openxlsx:Read, Write and Edit xlsx Files

Simplifies the creation of Excel .xlsx files by providing a high level interface to writing, styling and editing worksheets. Through the use of 'Rcpp', read/write times are comparable to the 'xlsx' and 'XLConnect' packages with the added benefit of removing the dependency on Java.

Maintained by Jan Marvin Garbuszus. Last updated 2 months ago.

xlsx cpp

13.3 match 232 stars 18.98 score 20k scripts 270 dependents

tbates

umx:Structural Equation Modeling and Twin Modeling in R

Quickly create, run, and report structural equation models, and twin models. See '?umx' for help, and umx_open_CRAN_page("umx") for NEWS. Timothy C. Bates, Michael C. Neale, Hermine H. Maes, (2019). umx: A library for Structural Equation and Twin Modelling in R. Twin Research and Human Genetics, 22, 27-41. <doi:10.1017/thg.2019.2>.

Maintained by Timothy C. Bates. Last updated 2 days ago.

behavior-genetics genetics openmx psychology sem statistics structural-equation-modeling tutorials twin-models umx

26.4 match 44 stars 9.45 score 472 scripts

bioc

OmnipathR:OmniPath web service client and more

A client for the OmniPath web service (https://www.omnipathdb.org) and many other resources. It also includes functions to transform and pretty print some of the downloaded data, functions to access a number of other resources such as BioPlex, ConsensusPathDB, EVEX, Gene Ontology, Guide to Pharmacology (IUPHAR/BPS), Harmonizome, HTRIdb, Human Phenotype Ontology, InWeb InBioMap, KEGG Pathway, Pathway Commons, Ramilowski et al. 2015, RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data, and its R implementation `nichenetr` (available only on github).

Maintained by Denes Turei. Last updated 19 days ago.

graphandnetwork network pathways software thirdpartyclient dataimport datarepresentation genesignaling generegulation systemsbiology transcriptomics singlecell annotation kegg complexes enzyme-ptm networks networks-biology omnipath proteins quarto

24.2 match 126 stars 9.90 score 226 scripts 2 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 8 hours ago.

complex-networks graph-algorithms graph-theory mathematics network-analysis network-graph fortran libxml2 glpk openblas cpp

10.9 match 582 stars 21.11 score 31k scripts 1.9k dependents

vincentarelbundock

countrycode:Convert Country Names and Country Codes

Standardize country names, convert them into one of 40 different coding schemes, convert between coding schemes, and assign region descriptors.

Maintained by Vincent Arel-Bundock. Last updated 3 months ago.

15.0 match 351 stars 14.80 score 6.3k scripts 119 dependents

gavinsimpson

gratia:Graceful 'ggplot'-Based Graphics and Other Functions for GAMs Fitted Using 'mgcv'

Graceful 'ggplot'-based graphics and utility functions for working with generalized additive models (GAMs) fitted using the 'mgcv' package. Provides a reimplementation of the plot() method for GAMs that 'mgcv' provides, as well as 'tidyverse' compatible representations of estimated smooths.

Maintained by Gavin L. Simpson. Last updated 8 hours ago.

distributional-regression gam gamm generalized-additive-mixed-models generalized-additive-models ggplot2 glm lm mgcv penalized-spline random-effects smoothing splines

16.4 match 217 stars 12.99 score 1.6k scripts 2 dependents

sfirke

janitor:Simple Tools for Examining and Cleaning Dirty Data

The main janitor functions can: perfectly format data.frame column names; provide quick counts of variable combinations (i.e., frequency tables and crosstabs); and explore duplicate records. Other janitor functions nicely format the tabulation results. These tabulate-and-report functions approximate popular features of SPSS and Microsoft Excel. This package follows the principles of the "tidyverse" and works well with the pipe function %>%. janitor was built with beginning-to-intermediate R users in mind and is optimized for user-friendliness.

Maintained by Sam Firke. Last updated 3 months ago.

data-analysis data-cleaning data-science dirty-data excel pivot-tables spss tabulations tidyverse

11.0 match 1.4k stars 19.15 score 35k scripts 231 dependents

traitecoevo

APCalign:Resolving Plant Taxon Names Using the Australian Plant Census

The process of resolving taxon names is necessary when working with biodiversity data. 'APCalign' uses the Australian Plant Census (APC) and the Australian Plant Name Index (APNI) to align and update plant taxon names to current, accepted standards. 'APCalign' also supplies information about the established status of plant taxa across different states/territories.

Maintained by Daniel Falster. Last updated 1 months ago.

28.9 match 4 stars 7.30 score 23 scripts 1 dependents

ropensci

ritis:Integrated Taxonomic Information System Client

An interface to the Integrated Taxonomic Information System ('ITIS') (<https://www.itis.gov>). Includes functions to work with the 'ITIS' REST API methods (<https://www.itis.gov/ws_description.html>), as well as the 'Solr' web service (<https://www.itis.gov/solr_documentation.html>).

Maintained by Julia Blum. Last updated 1 months ago.

taxonomy biology nomenclature json api web api-client identifiers species names api-wrapper itis taxize

27.1 match 16 stars 7.72 score 64 scripts 24 dependents

centerforassessment

randomNames:Generate Random Given and Surnames

Function for generating random gender and ethnicity correct first and/or last names. Names are chosen proportionally based upon their probability of appearing in a large scale data base of real names.

Maintained by Damian W. Betebenner. Last updated 3 months ago.

random-name-generators random-names

22.7 match 32 stars 9.24 score 297 scripts 5 dependents

mazamascience

MazamaSpatialUtils:Spatial Data Download and Utility Functions

A suite of conversion functions to create internally standardized spatial polygons data frames. Utility functions use these data sets to return values such as country, state, time zone, watershed, etc. associated with a set of longitude/latitude pairs. (They also make cool maps.)

Maintained by Jonathan Callahan. Last updated 5 months ago.

25.8 match 5 stars 8.09 score 282 scripts 2 dependents

cran

nlme:Linear and Nonlinear Mixed Effects Models

Fit and compare Gaussian linear and nonlinear mixed-effects models.

Maintained by R Core Team. Last updated 2 months ago.

fortran

16.0 match 6 stars 13.00 score 13k scripts 8.7k dependents

bioc

Biobase:Biobase: Base functions for Bioconductor

Functions that are needed by many other packages or which replace R functions.

Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.

infrastructure bioconductor-package core-package

12.6 match 9 stars 16.45 score 6.6k scripts 1.8k dependents

darwin-eu

omopgenerics:Methods and Classes for the OMOP Common Data Model

Provides definitions of core classes and methods used by analytic pipelines that query the OMOP (Observational Medical Outcomes Partnership) common data model.

Maintained by Martí Català. Last updated 9 days ago.

20.8 match 9.97 score 193 scripts 16 dependents

mappinguniverse

mapping:Automatic Download, Linking, Manipulating Coordinates for Maps

Maps are an important tool to visualise variables distribution across different spatial objects. The mapping process requires to link the data with coordinates and then generate the correspondent map. This package provide coordinates, linking and mapping functions for an automatic, flexible and easy approach of external functions. The package provides an easy, flexible and automatic unit. Geographical coordinates are provided in the package and automatically linked with the input data to generate maps with internal provided functions or external functions. Provide an easy, flexible and automatic approach to potentially download updated coordinates, to link statistical units with coordinates and to aggregate variables based on the spatial hierarchy of units. The object returned from the package can be used for thematic maps with the build-in functions provided in mapping or with other packages already available.

Maintained by Alessio Serafini. Last updated 1 years ago.

43.0 match 4 stars 4.79 score 31 scripts

bioc

RCy3:Functions to Access and Control Cytoscape

Vizualize, analyze and explore networks using Cytoscape via R. Anything you can do using the graphical user interface of Cytoscape, you can now do with a single RCy3 function.

Maintained by Alex Pico. Last updated 5 months ago.

visualization graphandnetwork thirdpartyclient network

15.4 match 52 stars 13.39 score 628 scripts 15 dependents

bioc

ORFik:Open Reading Frames in Genomics

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

Maintained by Haakon Tjeldnes. Last updated 27 days ago.

immunooncology software sequencing riboseq rnaseq functionalgenomics coverage alignment dataimport cpp

19.3 match 33 stars 10.63 score 115 scripts 2 dependents

sherrillmix

taxonomizr:Functions to Work with NCBI Accessions and Taxonomy

Functions for assigning taxonomy to NCBI accession numbers and taxon IDs based on NCBI's accession2taxid and taxdump files. This package allows the user to download NCBI data dumps and create a local database for fast and local taxonomic assignment.

Maintained by Scott Sherrill-Mix. Last updated 4 days ago.

22.8 match 72 stars 8.85 score 255 scripts 2 dependents

skranz

RTutor:Interactive R problem sets with automatic testing of solutions and automatic hints

Interactive R problem sets with automatic testing of solutions and automatic hints

Maintained by Sebastian Kranz. Last updated 1 years ago.

economics learn-to-code problem-set rstudio rtutor shiny teaching

33.7 match 205 stars 5.83 score 111 scripts 1 dependents

niaid

dsb:Normalize & Denoise Droplet Single Cell Protein Data (CITE-Seq)

This lightweight R package provides a method for normalizing and denoising protein expression data from droplet based single cell experiments. Raw protein Unique Molecular Index (UMI) counts from sequencing DNA-conjugated antibody derived tags (ADT) in droplets (e.g. 'CITE-seq') have substantial measurement noise. Our experiments and computational modeling revealed two major components of this noise: 1) protein-specific noise originating from ambient, unbound antibody encapsulated in droplets that can be accurately inferred via the expected protein counts detected in empty droplets, and 2) droplet/cell-specific noise revealed via the shared variance component associated with isotype antibody controls and background protein counts in each cell. This package normalizes and removes both of these sources of noise from raw protein data derived from methods such as 'CITE-seq', 'REAP-seq', 'ASAP-seq', 'TEA-seq', 'proteogenomic' data from the Mission Bio platform, etc. See the vignette for tutorials on how to integrate dsb with 'Seurat' and 'Bioconductor' and how to use dsb in 'Python'. Please see our paper Mulè M.P., Martins A.J., and Tsang J.S. Nature Communications 2022 <https://www.nature.com/articles/s41467-022-29356-8> for more details on the method.

Maintained by Matthew Mulè. Last updated 9 months ago.

cite-seq niaid-tsang-lab

25.4 match 65 stars 7.73 score 104 scripts

dfsp-spirit

fsbrain:Managing and Visualizing Brain Surface Data

Provides high-level access to neuroimaging data from standard software packages like 'FreeSurfer' <http://freesurfer.net/> on the level of subjects and groups. Load morphometry data, surfaces and brain parcellations based on atlases. Mask data using labels, load data for specific atlas regions only, and visualize data and statistical results directly in 'R'.

Maintained by Tim Schäfer. Last updated 4 months ago.

3d brain dti freesurfer mesh mri neuroimaging research surface visualization voxel

29.8 match 66 stars 6.47 score 15 scripts

trinker

lexicon:Lexicons for Text Analysis

A collection of lexical hash tables, dictionaries, and word lists.

Maintained by Tyler Rinker. Last updated 3 years ago.

hash lexicon lookup names-frequent stopwords text-dictionaries text-mining

21.8 match 111 stars 8.80 score 224 scripts 25 dependents

tomasfryda

h2o:R Interface for the 'H2O' Scalable Machine Learning Platform

R interface for 'H2O', the scalable open source machine learning platform that offers parallelized implementations of many supervised and unsupervised machine learning algorithms such as Generalized Linear Models (GLM), Gradient Boosting Machines (including XGBoost), Random Forests, Deep Neural Networks (Deep Learning), Stacked Ensembles, Naive Bayes, Generalized Additive Models (GAM), ANOVA GLM, Cox Proportional Hazards, K-Means, PCA, ModelSelection, Word2Vec, as well as a fully automatic machine learning algorithm (H2O AutoML).

Maintained by Tomas Fryda. Last updated 1 years ago.

22.9 match 3 stars 8.20 score 7.8k scripts 11 dependents

cran

compositions:Compositional Data Analysis

Provides functions for the consistent analysis of compositional data (e.g. portions of substances) and positive numbers (e.g. concentrations) in the way proposed by J. Aitchison and V. Pawlowsky-Glahn.

Maintained by K. Gerald van den Boogaart. Last updated 1 years ago.

openblas

29.3 match 1 stars 6.35 score 36 dependents

bioc

rWikiPathways:rWikiPathways - R client library for the WikiPathways API

Use this package to interface with the WikiPathways API. It provides programmatic access to WikiPathways content in multiple data and image formats, including official monthly release files and convenient GMT read/write functions.

Maintained by Egon Willighagen. Last updated 5 months ago.

visualization graphandnetwork thirdpartyclient network metabolomics bioinformatics data-access pathways

19.9 match 15 stars 9.23 score 131 scripts 3 dependents

wraff

wrMisc:Analyze Experimental High-Throughput (Omics) Data

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

Maintained by Wolfgang Raffelsberger. Last updated 7 months ago.

41.3 match 4.44 score 33 scripts 4 dependents

sjmack

HLAtools:Toolkit for HLA Immunogenomics

A toolkit for the analysis and management of data for genes in the so-called "Human Leukocyte Antigen" (HLA) region. Functions extract reference data from the Anthony Nolan HLA Informatics Group/ImmunoGeneTics HLA 'GitHub' repository (ANHIG/IMGTHLA) <https://github.com/ANHIG/IMGTHLA>, validate Genotype List (GL) Strings, convert between UNIFORMAT and GL String Code (GLSC) formats, translate HLA alleles and GLSCs across ImmunoPolymorphism Database (IPD) IMGT/HLA Database release versions, identify differences between pairs of alleles at a locus, generate customized, multi-position sequence alignments, trim and convert allele-names across nomenclature epochs, and extend existing data-analysis methods.

Maintained by Steven Mack. Last updated 13 days ago.

29.4 match 4 stars 6.21 score 7 scripts 1 dependents

renkun-ken

rlist:A Toolbox for Non-Tabular Data Manipulation

Provides a set of functions for data manipulation with list objects, including mapping, filtering, grouping, sorting, updating, searching, and other useful functions. Most functions are designed to be pipeline friendly so that data processing with lists can be chained.

Maintained by Kun Ren. Last updated 2 years ago.

13.2 match 206 stars 13.73 score 2.2k scripts 123 dependents

r-dbi

DBI:R Database Interface

A database interface definition for communication between R and relational database management systems. All classes in this package are virtual and need to be extended by the various R/DBMS implementations.

Maintained by Kirill Müller. Last updated 3 months ago.

database interface

8.7 match 302 stars 20.88 score 19k scripts 2.9k dependents

cvxgrp

CVXR:Disciplined Convex Optimization

An object-oriented modeling language for disciplined convex programming (DCP) as described in Fu, Narasimhan, and Boyd (2020, <doi:10.18637/jss.v094.i14>). It allows the user to formulate convex optimization problems in a natural way following mathematical convention and DCP rules. The system analyzes the problem, verifies its convexity, converts it into a canonical form, and hands it off to an appropriate solver to obtain the solution. Interfaces to solvers on CRAN and elsewhere are provided, both commercial and open source.

Maintained by Anqi Fu. Last updated 4 months ago.

cpp

13.9 match 207 stars 12.89 score 768 scripts 51 dependents

alexpkeil1

qgcomp:Quantile G-Computation

G-computation for a set of time-fixed exposures with quantile-based basis functions, possibly under linearity and homogeneity assumptions. This approach estimates a regression line corresponding to the expected change in the outcome (on the link basis) given a simultaneous increase in the quantile-based category for all exposures. Works with continuous, binary, and right-censored time-to-event outcomes. Reference: Alexander P. Keil, Jessie P. Buckley, Katie M. OBrien, Kelly K. Ferguson, Shanshan Zhao, and Alexandra J. White (2019) A quantile-based g-computation approach to addressing the effects of exposure mixtures; <doi:10.1289/EHP5838>.

Maintained by Alexander Keil. Last updated 4 days ago.

exposure exposure-mixture exposure-mixtures quantile-gcomputation survival

20.2 match 37 stars 8.73 score 70 scripts 2 dependents

crunch-io

crunch:Crunch.io Data Tools

The Crunch.io service <https://crunch.io/> provides a cloud-based data store and analytic engine, as well as an intuitive web interface. Using this package, analysts can interact with and manipulate Crunch datasets from within R. Importantly, this allows technical researchers to collaborate naturally with team members, managers, and clients who prefer a point-and-click interface.

Maintained by Greg Freedman Ellis. Last updated 11 days ago.

16.7 match 9 stars 10.53 score 200 scripts 2 dependents

pecanproject

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

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

Maintained by David LeBauer. Last updated 2 days ago.

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

14.8 match 216 stars 11.88 score 127 scripts 27 dependents

spatstat

spatstat.geom:Geometrical Functionality of the 'spatstat' Family

Defines spatial data types and supports geometrical operations on them. Data types include point patterns, windows (domains), pixel images, line segment patterns, tessellations and hyperframes. Capabilities include creation and manipulation of data (using command line or graphical interaction), plotting, geometrical operations (rotation, shift, rescale, affine transformation), convex hull, discretisation and pixellation, Dirichlet tessellation, Delaunay triangulation, pairwise distances, nearest-neighbour distances, distance transform, morphological operations (erosion, dilation, closing, opening), quadrat counting, geometrical measurement, geometrical covariance, colour maps, calculus on spatial domains, Gaussian blur, level sets of images, transects of images, intersections between objects, minimum distance matching. (Excludes spatial data on a network, which are supported by the package 'spatstat.linnet'.)

Maintained by Adrian Baddeley. Last updated 2 days ago.

classes-and-objects distance-calculation geometry geometry-processing images mensuration plotting point-patterns spatial-data spatial-data-analysis

14.3 match 7 stars 12.11 score 241 scripts 227 dependents

tidyverse

tidyr:Tidy Messy Data

Tools to help to create tidy data, where each column is a variable, each row is an observation, and each cell contains a single value. 'tidyr' contains tools for changing the shape (pivoting) and hierarchy (nesting and 'unnesting') of a dataset, turning deeply nested lists into rectangular data frames ('rectangling'), and extracting values out of string columns. It also includes tools for working with missing values (both implicit and explicit).

Maintained by Hadley Wickham. Last updated 13 days ago.

tidy-data cpp

7.5 match 1.4k stars 22.88 score 168k scripts 5.5k dependents

berndbischl

BBmisc:Miscellaneous Helper Functions for B. Bischl

Miscellaneous helper functions for and from B. Bischl and some other guys, mainly for package development.

Maintained by Bernd Bischl. Last updated 2 years ago.

15.9 match 20 stars 10.59 score 980 scripts 69 dependents

hrbrmstr

hrbrthemes:Additional Themes, Theme Components and Utilities for 'ggplot2'

A compilation of extra 'ggplot2' themes, scales and utilities, including a spell check function for plot label fields and an overall emphasis on typography. A copy of the 'Google' font 'Roboto Condensed' is also included.

Maintained by Bob Rudis. Last updated 2 days ago.

data-visualization datavisualization ggplot-extension ggplot2 ggplot2-scales ggplot2-themes visualization

12.0 match 1.3k stars 13.92 score 13k scripts 15 dependents

eitsupi

neopolars:R Bindings for the 'polars' Rust 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 Tatsuya Shima. Last updated 1 days ago.

rust cargo

34.4 match 40 stars 4.86 score 1 scripts

r-lib

tidyselect:Select from a Set of Strings

A backend for the selecting functions of the 'tidyverse'. It makes it easy to implement select-like functions in your own packages in a way that is consistent with other 'tidyverse' interfaces for selection.

Maintained by Lionel Henry. Last updated 3 months ago.

9.1 match 130 stars 18.31 score 1.9k scripts 8.2k dependents

tanaylab

naryn:Native Access Medical Record Retriever for High Yield Analytics

A toolkit for medical records data analysis. The 'naryn' package implements an efficient data structure for storing medical records, and provides a set of functions for data extraction, manipulation and analysis.

Maintained by Aviezer Lifshitz. Last updated 4 days ago.

data-analysis medical-records cpp

31.5 match 3 stars 5.26 score 4 scripts

bioc

gDRutils:A package with helper functions for processing drug response data

This package contains utility functions used throughout the gDR platform to fit data, manipulate data, and convert and validate data structures. This package also has the necessary default constants for gDR platform. Many of the functions are utilized by the gDRcore package.

Maintained by Arkadiusz Gladki. Last updated 4 days ago.

software infrastructure

22.2 match 2 stars 7.40 score 3 scripts 3 dependents

cmmr

rbiom:Read/Write, Analyze, and Visualize 'BIOM' Data

A toolkit for working with Biological Observation Matrix ('BIOM') files. Read/write all 'BIOM' formats. Compute rarefaction, alpha diversity, and beta diversity (including 'UniFrac'). Summarize counts by taxonomic level. Subset based on metadata. Generate visualizations and statistical analyses. CPU intensive operations are coded in C for speed.

Maintained by Daniel P. Smith. Last updated 6 days ago.

18.1 match 15 stars 9.02 score 117 scripts 6 dependents

ropensci

taxadb:A High-Performance Local Taxonomic Database Interface

Creates a local database of many commonly used taxonomic authorities and provides functions that can quickly query this data.

Maintained by Carl Boettiger. Last updated 11 months ago.

21.1 match 43 stars 7.68 score 53 scripts 1 dependents

cran

XML:Tools for Parsing and Generating XML Within R and S-Plus

Many approaches for both reading and creating XML (and HTML) documents (including DTDs), both local and accessible via HTTP or FTP. Also offers access to an 'XPath' "interpreter".

Maintained by CRAN Team. Last updated 2 months ago.

libxml2

18.2 match 3 stars 8.87 score 1.3k dependents

mihai-sysbio

glpkAPI:R Interface to C API of GLPK

R Interface to C API of GLPK, depends on GLPK Version >= 4.42.

Maintained by Mihail Anton. Last updated 2 years ago.

glpk

27.1 match 5.96 score 51 scripts 12 dependents

rspatial

terra:Spatial Data Analysis

Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).

Maintained by Robert J. Hijmans. Last updated 20 hours ago.

geospatial raster spatial vector onetbb proj gdal geos cpp

9.1 match 559 stars 17.64 score 17k scripts 851 dependents

andrisignorell

DescTools:Tools for Descriptive Statistics

A collection of miscellaneous basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'BigCamelCase' style was consequently applied to functions borrowed from contributed R packages as well.

Maintained by Andri Signorell. Last updated 5 hours ago.

fortran cpp

9.6 match 87 stars 16.70 score 7.7k scripts 99 dependents

ropensci

worrms:World Register of Marine Species (WoRMS) Client

Client for World Register of Marine Species (<https://www.marinespecies.org/>). Includes functions for each of the API methods, including searching for names by name, date and common names, searching using external identifiers, fetching synonyms, as well as fetching taxonomic children and taxonomic classification.

Maintained by Bart Vanhoorne.. Last updated 1 years ago.

biology science marine api web api-client worms species api-wrapper biological-data fish jerico-relevant marine-biology marine-species taxize taxonomy

16.0 match 27 stars 9.79 score 372 scripts 23 dependents

irworkshop

campfin:Wrangle Campaign Finance Data

Explore and normalize American campaign finance data. Created by the Investigative Reporting Workshop to facilitate work on The Accountability Project, an effort to collect public data into a central, standard database that is more easily searched: <https://publicaccountability.org/>.

Maintained by Kiernan Nicholls. Last updated 1 years ago.

campaign-finance data-journalism

27.3 match 17 stars 5.66 score 54 scripts

christopherkenny

censable:Making Census Data More Usable

Creates a common framework for organizing, naming, and gathering population, age, race, and ethnicity data from the Census Bureau. Accesses the API <https://www.census.gov/data/developers/data-sets.html>. Provides tools for adding information to existing data to line up with Census data.

Maintained by Christopher T. Kenny. Last updated 10 months ago.

26.4 match 8 stars 5.78 score 42 scripts 4 dependents

jangraffelman

HardyWeinberg:Statistical Tests and Graphics for Hardy-Weinberg Equilibrium

Contains tools for exploring Hardy-Weinberg equilibrium (Hardy, 1908; Weinberg, 1908) for bi and multi-allelic genetic marker data. All classical tests (chi-square, exact, likelihood-ratio and permutation tests) with bi-allelic variants are included in the package, as well as functions for power computation and for the simulation of marker data under equilibrium and disequilibrium. Routines for dealing with markers on the X-chromosome are included (Graffelman & Weir, 2016) <doi:10.1038/hdy.2016.20>, including Bayesian procedures. Some exact and permutation procedures also work with multi-allelic variants. Special test procedures that jointly address Hardy-Weinberg equilibrium and equality of allele frequencies in both sexes are supplied, for the bi and multi-allelic case. Functions for testing equilibrium in the presence of missing data by using multiple imputation are also provided. Implements several graphics for exploring the equilibrium status of a large set of bi-allelic markers: ternary plots with acceptance regions, log-ratio plots and Q-Q plots. The functionality of the package is explained in detail in a related JSS paper <doi:10.18637/jss.v064.i03>.

Maintained by Jan Graffelman. Last updated 11 months ago.

cpp

24.1 match 6.30 score 167 scripts 4 dependents

venelin

PCMBase:Simulation and Likelihood Calculation of Phylogenetic Comparative Models

Phylogenetic comparative methods represent models of continuous trait data associated with the tips of a phylogenetic tree. Examples of such models are Gaussian continuous time branching stochastic processes such as Brownian motion (BM) and Ornstein-Uhlenbeck (OU) processes, which regard the data at the tips of the tree as an observed (final) state of a Markov process starting from an initial state at the root and evolving along the branches of the tree. The PCMBase R package provides a general framework for manipulating such models. This framework consists of an application programming interface for specifying data and model parameters, and efficient algorithms for simulating trait evolution under a model and calculating the likelihood of model parameters for an assumed model and trait data. The package implements a growing collection of models, which currently includes BM, OU, BM/OU with jumps, two-speed OU as well as mixed Gaussian models, in which different types of the above models can be associated with different branches of the tree. The PCMBase package is limited to trait-simulation and likelihood calculation of (mixed) Gaussian phylogenetic models. The PCMFit package provides functionality for inference of these models to tree and trait data. The package web-site <https://venelin.github.io/PCMBase/> provides access to the documentation and other resources.

Maintained by Venelin Mitov. Last updated 10 months ago.

20.0 match 6 stars 7.56 score 85 scripts 3 dependents

mlizhangx

NAIR:Network Analysis of Immune Repertoire

Pipelines for studying the adaptive immune repertoire of T cells and B cells via network analysis based on receptor sequence similarity. Relate clinical outcomes to immune repertoires based on their network properties, or to particular clusters and clones within a repertoire. Yang et al. (2023) <doi:10.3389/fimmu.2023.1181825>.

Maintained by Brian Neal. Last updated 2 months ago.

cpp openmp

21.8 match 7 stars 6.83 score 27 scripts

blasbenito

distantia:Advanced Toolset for Efficient Time Series Dissimilarity Analysis

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

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

25.5 match 23 stars 5.76 score 11 scripts

egenn

rtemis:Machine Learning and Visualization

Advanced Machine Learning and Visualization. Unsupervised Learning (Clustering, Decomposition), Supervised Learning (Classification, Regression), Cross-Decomposition, Bagging, Boosting, Meta-models. Static and interactive graphics.

Maintained by E.D. Gennatas. Last updated 1 months ago.

data-science data-visualization machine-learning machine-learning-library visualization

20.5 match 145 stars 7.09 score 50 scripts 2 dependents

r-lib

available:Check if the Title of a Package is Available, Appropriate and Interesting

Check if a given package name is available to use. It checks the name's validity. Checks if it is used on 'GitHub', 'CRAN' and 'Bioconductor'. Checks for unintended meanings by querying 'Wiktionary' and Wikipedia.

Maintained by Gábor Csárdi. Last updated 7 months ago.

unconf unconf17

17.6 match 145 stars 8.25 score 119 scripts 4 dependents

grunwaldlab

metacoder:Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

Reads, plots, and manipulates large taxonomic data sets, like those generated from modern high-throughput sequencing, such as metabarcoding (i.e. amplification metagenomics, 16S metagenomics, etc). It provides a tree-based visualization called "heat trees" used to depict statistics for every taxon in a taxonomy using color and size. It also provides various functions to do common tasks in microbiome bioinformatics on data in the 'taxmap' format defined by the 'taxa' package. The 'metacoder' package is described in the publication by Foster et al. (2017) <doi:10.1371/journal.pcbi.1005404>.

Maintained by Zachary Foster. Last updated 1 months ago.

community-diversity hierarchical metabarcoding pcr taxonomy trees cpp

14.9 match 140 stars 9.64 score 328 scripts

stemangiola

tidyHeatmap:A Tidy Implementation of Heatmap

This is a tidy implementation for heatmap. At the moment it is based on the (great) package 'ComplexHeatmap'. The goal of this package is to interface a tidy data frame with this powerful tool. Some of the advantages are: Row and/or columns colour annotations are easy to integrate just specifying one parameter (column names). Custom grouping of rows is easy to specify providing a grouped tbl. For example: df %>% group_by(...). Labels size adjusted by row and column total number. Default use of Brewer and Viridis palettes.

Maintained by Stefano Mangiola. Last updated 1 months ago.

assaydomain infrastructure brewer complexheatmap custom-palette dplyr graphviz heatmap mtcars plotting rstudio scale tibble tidy tidy-data-frame tidybulk tidyverse viridis

14.0 match 335 stars 10.23 score 197 scripts 1 dependents

rhartmano

labelr:Label Data Frames, Variables, and Values

Create and use data frame labels for data frame objects (frame labels), their columns (name labels), and individual values of a column (value labels). Value labels include one-to-one and many-to-one labels for nominal and ordinal variables, as well as numerical range-based value labels for continuous variables. Convert value-labeled variables so each value is replaced by its corresponding value label. Add values-converted-to-labels columns to a value-labeled data frame while preserving parent columns. Filter and subset a value-labeled data frame using labels, while returning results in terms of values. Overlay labels in place of values in common R commands to increase interpretability. Generate tables of value frequencies, with categories expressed as raw values or as labels. Access data frames that show value-to-label mappings for easy reference.

Maintained by Robert Hartman. Last updated 7 months ago.

25.2 match 3 stars 5.65 score 10 scripts

tidyverse

dplyr:A Grammar of Data Manipulation

A fast, consistent tool for working with data frame like objects, both in memory and out of memory.

Maintained by Hadley Wickham. Last updated 13 days ago.

data-manipulation grammar cpp

5.8 match 4.8k stars 24.68 score 659k scripts 7.8k dependents

josesamos

rolap:Obtaining Star Databases from Flat Tables

Data in multidimensional systems is obtained from operational systems and is transformed to adapt it to the new structure. Frequently, the operations to be performed aim to transform a flat table into a ROLAP (Relational On-Line Analytical Processing) star database. The main objective of the package is to allow the definition of these transformations easily. The implementation of the multidimensional database obtained can be exported to work with multidimensional analysis tools on spreadsheets or relational databases.

Maintained by Jose Samos. Last updated 1 years ago.

openjdk

22.6 match 5 stars 6.12 score 25 scripts 1 dependents

amices

mice:Multivariate Imputation by Chained Equations

Multiple imputation using Fully Conditional Specification (FCS) implemented by the MICE algorithm as described in Van Buuren and Groothuis-Oudshoorn (2011) <doi:10.18637/jss.v045.i03>. Each variable has its own imputation model. Built-in imputation models are provided for continuous data (predictive mean matching, normal), binary data (logistic regression), unordered categorical data (polytomous logistic regression) and ordered categorical data (proportional odds). MICE can also impute continuous two-level data (normal model, pan, second-level variables). Passive imputation can be used to maintain consistency between variables. Various diagnostic plots are available to inspect the quality of the imputations.

Maintained by Stef van Buuren. Last updated 6 days ago.

chained-equations fcs imputation mice missing-data missing-values multiple-imputation multivariate-data cpp

8.4 match 462 stars 16.50 score 10k scripts 154 dependents

tyee001

VGAM:Vector Generalized Linear and Additive Models

An implementation of about 6 major classes of statistical regression models. The central algorithm is Fisher scoring and iterative reweighted least squares. At the heart of this package are the vector generalized linear and additive model (VGLM/VGAM) classes. VGLMs can be loosely thought of as multivariate GLMs. VGAMs are data-driven VGLMs that use smoothing. The book "Vector Generalized Linear and Additive Models: With an Implementation in R" (Yee, 2015) <DOI:10.1007/978-1-4939-2818-7> gives details of the statistical framework and the package. Currently only fixed-effects models are implemented. Many (100+) models and distributions are estimated by maximum likelihood estimation (MLE) or penalized MLE. The other classes are RR-VGLMs (reduced-rank VGLMs), quadratic RR-VGLMs, doubly constrained RR-VGLMs, quadratic RR-VGLMs, reduced-rank VGAMs, RCIMs (row-column interaction models)---these classes perform constrained and unconstrained quadratic ordination (CQO/UQO) models in ecology, as well as constrained additive ordination (CAO). Hauck-Donner effect detection is implemented. Note that these functions are subject to change; see the NEWS and ChangeLog files for latest changes.

Maintained by Thomas Yee. Last updated 1 months ago.

fortran

12.8 match 10 stars 10.67 score 3.6k scripts 169 dependents

bioc

singleCellTK:Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

The Single Cell Toolkit (SCTK) in the singleCellTK package provides an interface to popular tools for importing, quality control, analysis, and visualization of single cell RNA-seq data. SCTK allows users to seamlessly integrate tools from various packages at different stages of the analysis workflow. A general "a la carte" workflow gives users the ability access to multiple methods for data importing, calculation of general QC metrics, doublet detection, ambient RNA estimation and removal, filtering, normalization, batch correction or integration, dimensionality reduction, 2-D embedding, clustering, marker detection, differential expression, cell type labeling, pathway analysis, and data exporting. Curated workflows can be used to run Seurat and Celda. Streamlined quality control can be performed on the command line using the SCTK-QC pipeline. Users can analyze their data using commands in the R console or by using an interactive Shiny Graphical User Interface (GUI). Specific analyses or entire workflows can be summarized and shared with comprehensive HTML reports generated by Rmarkdown. Additional documentation and vignettes can be found at camplab.net/sctk.

Maintained by Joshua David Campbell. Last updated 24 days ago.

singlecell geneexpression differentialexpression alignment clustering immunooncology batcheffect normalization qualitycontrol dataimport gui

13.4 match 181 stars 10.16 score 252 scripts

alistaire47

passport:Travel Smoothly Between Country Name and Code Formats

Smooths the process of working with country names and codes via powerful parsing, standardization, and conversion utilities arranged in a simple, consistent API. Country name formats include multiple sources including the Unicode Common Locale Data Repository (CLDR, <http://cldr.unicode.org/>) common-sense standardized names in hundreds of languages.

Maintained by Edward Visel. Last updated 4 years ago.

country-codes country-data country-names

21.9 match 35 stars 6.17 score 28 scripts 1 dependents

adeverse

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

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

Maintained by Aurélie Siberchicot. Last updated 12 days ago.

openblas cpp

9.0 match 39 stars 14.96 score 2.2k scripts 256 dependents

billdenney

PKNCA:Perform Pharmacokinetic Non-Compartmental Analysis

Compute standard Non-Compartmental Analysis (NCA) parameters for typical pharmacokinetic analyses and summarize them.

Maintained by Bill Denney. Last updated 16 days ago.

nca noncompartmental-analysis pharmacokinetics

10.7 match 73 stars 12.61 score 214 scripts 4 dependents

kharchenkolab

pagoda2:Single Cell Analysis and Differential Expression

Analyzing and interactively exploring large-scale single-cell RNA-seq datasets. 'pagoda2' primarily performs normalization and differential gene expression analysis, with an interactive application for exploring single-cell RNA-seq datasets. It performs basic tasks such as cell size normalization, gene variance normalization, and can be used to identify subpopulations and run differential expression within individual samples. 'pagoda2' was written to rapidly process modern large-scale scRNAseq datasets of approximately 1e6 cells. The companion web application allows users to explore which gene expression patterns form the different subpopulations within your data. The package also serves as the primary method for preprocessing data for conos, <https://github.com/kharchenkolab/conos>. This package interacts with data available through the 'p2data' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/pagoda2>. The size of the 'p2data' package is approximately 6 MB.

Maintained by Evan Biederstedt. Last updated 1 years ago.

scrna-seq single-cell single-cell-rna-seq transcriptomics openblas cpp openmp

16.8 match 222 stars 8.00 score 282 scripts

nacnudus

tidyxl:Read Untidy Excel Files

Imports non-tabular from Excel files into R. Exposes cell content, position and formatting in a tidy structure for further manipulation. Tokenizes Excel formulas. Supports '.xlsx' and '.xlsm' via the embedded 'RapidXML' C++ library <https://rapidxml.sourceforge.net>. Does not support '.xlsb' or '.xls'.

Maintained by Duncan Garmonsway. Last updated 1 years ago.

excelreader rcpp spreadsheet tidy cpp

12.5 match 251 stars 10.69 score 382 scripts 13 dependents

henrikbengtsson

R.utils:Various Programming Utilities

Utility functions useful when programming and developing R packages.

Maintained by Henrik Bengtsson. Last updated 1 years ago.

9.7 match 63 stars 13.74 score 5.7k scripts 814 dependents

darwin-eu

PatientProfiles:Identify Characteristics of Patients in the OMOP Common Data Model

Identify the characteristics of patients in data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model.

Maintained by Marti Catala. Last updated 9 days ago.

13.4 match 1 stars 9.97 score 225 scripts 9 dependents

easystats

datawizard:Easy Data Wrangling and Statistical Transformations

A lightweight package to assist in key steps involved in any data analysis workflow: (1) wrangling the raw data to get it in the needed form, (2) applying preprocessing steps and statistical transformations, and (3) compute statistical summaries of data properties and distributions. It is also the data wrangling backend for packages in 'easystats' ecosystem. References: Patil et al. (2022) <doi:10.21105/joss.04684>.

Maintained by Etienne Bacher. Last updated 9 days ago.

data dplyr hacktoberfest janitor manipulation reshape tidyr wrangling

9.1 match 222 stars 14.71 score 436 scripts 119 dependents

ropensci

rotl:Interface to the 'Open Tree of Life' API

An interface to the 'Open Tree of Life' API to retrieve phylogenetic trees, information about studies used to assemble the synthetic tree, and utilities to match taxonomic names to 'Open Tree identifiers'. The 'Open Tree of Life' aims at assembling a comprehensive phylogenetic tree for all named species.

Maintained by Francois Michonneau. Last updated 2 years ago.

metadata ropensci phylogenetics independant-contrasts biodiversity peer-reviewed phylogeny taxonomy

11.0 match 40 stars 12.05 score 356 scripts 29 dependents

satijalab

SeuratObject:Data Structures for Single Cell Data

Defines S4 classes for single-cell genomic data and associated information, such as dimensionality reduction embeddings, nearest-neighbor graphs, and spatially-resolved coordinates. Provides data access methods and R-native hooks to ensure the Seurat object is familiar to other R users. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031> for more details.

Maintained by Paul Hoffman. Last updated 1 years ago.

cpp

11.3 match 25 stars 11.69 score 1.2k scripts 88 dependents

insightsengineering

chevron:Standard TLGs for Clinical Trials Reporting

Provide standard tables, listings, and graphs (TLGs) libraries used in clinical trials. This package implements a structure to reformat the data with 'dunlin', create reporting tables using 'rtables' and 'tern' with standardized input arguments to enable quick generation of standard outputs. In addition, it also provides comprehensive data checks and script generation functionality.

Maintained by Joe Zhu. Last updated 24 days ago.

clinical-trials graphs listings nest reporting tables

16.0 match 12 stars 8.24 score 12 scripts

bromaghin

qfasar:Quantitative Fatty Acid Signature Analysis in R

An implementation of Quantitative Fatty Acid Signature Analysis (QFASA) in R. QFASA is a method of estimating the diet composition of predators. The fundamental unit of information in QFASA is a fatty acid signature (signature), which is a vector of proportions describing the composition of fatty acids within lipids. Signature data from at least one predator and from samples of all potential prey types are required. Calibration coefficients, which adjust for the differential metabolism of individual fatty acids by predators, are also required. Given those data inputs, a predator signature is modeled as a mixture of prey signatures and its diet estimate is obtained as the mixture that minimizes a measure of distance between the observed and modeled signatures. A variety of estimation options and simulation capabilities are implemented. Please refer to the vignette for additional details and references.

Maintained by Jeffrey F. Bromaghin. Last updated 5 years ago.

43.8 match 2.90 score 40 scripts

spedygiorgio

markovchain:Easy Handling Discrete Time Markov Chains

Functions and S4 methods to create and manage discrete time Markov chains more easily. In addition functions to perform statistical (fitting and drawing random variates) and probabilistic (analysis of their structural proprieties) analysis are provided. See Spedicato (2017) <doi:10.32614/RJ-2017-036>. Some functions for continuous times Markov chains depend on the suggested ctmcd package.

Maintained by Giorgio Alfredo Spedicato. Last updated 4 months ago.

ctmc dtmc markov-chain markov-model r-programming rcpp openblas cpp

9.9 match 104 stars 12.78 score 712 scripts 4 dependents

dmurdoch

rgl:3D Visualization Using OpenGL

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

Maintained by Duncan Murdoch. Last updated 2 months ago.

graphics opengl rgl webgl libglu libglvnd libpng libx11 freetype cpp

7.2 match 91 stars 17.49 score 7.3k scripts 300 dependents

usepa

tcpl:ToxCast Data Analysis Pipeline

The ToxCast Data Analysis Pipeline ('tcpl') is an R package that manages, curve-fits, plots, and stores ToxCast data to populate its linked MySQL database, 'invitrodb'. The package was developed for the chemical screening data curated by the US EPA's Toxicity Forecaster (ToxCast) program, but 'tcpl' can be used to support diverse chemical screening efforts.

Maintained by Jason Brown. Last updated 3 days ago.

ccte comptox ord

13.4 match 36 stars 9.41 score 90 scripts

jimmyday12

fitzRoy:Easily Scrape and Process AFL Data

An easy package for scraping and processing Australia Rules Football (AFL) data. 'fitzRoy' provides a range of functions for accessing publicly available data from 'AFL Tables' <https://afltables.com/afl/afl_index.html>, 'Footy Wire' <https://www.footywire.com> and 'The Squiggle' <https://squiggle.com.au>. Further functions allow for easy processing, cleaning and transformation of this data into formats that can be used for analysis.

Maintained by James Day. Last updated 2 months ago.

11.5 match 134 stars 10.74 score 324 scripts

alexpkeil1

qgcompint:Quantile G-Computation Extensions for Effect Measure Modification

G-computation for a set of time-fixed exposures with quantile-based basis functions, possibly under linearity and homogeneity assumptions. Effect measure modification in this method is a way to assess how the effect of the mixture varies by a binary, categorical or continuous variable. Reference: Alexander P. Keil, Jessie P. Buckley, Katie M. OBrien, Kelly K. Ferguson, Shanshan Zhao, and Alexandra J. White (2019) A quantile-based g-computation approach to addressing the effects of exposure mixtures; <doi:10.1289/EHP5838>.

Maintained by Alexander Keil. Last updated 4 days ago.

25.2 match 4 stars 4.89 score 13 scripts

bradduthie

resevol:Simulate Agricultural Production and Evolution of Pesticide Resistance

Simulates individual-based models of agricultural pest management and the evolution of pesticide resistance. Management occurs on a spatially explicit landscape that is divided into an arbitrary number of farms that can grow one of up to 10 crops and apply one of up to 10 pesticides. Pest genomes are modelled in a way that allows for any number of pest traits with an arbitrary covariance structure that is constructed using an evolutionary algorithm in the mine_gmatrix() function. Simulations are then run using the run_farm_sim() function. This package thereby allows for highly mechanistic social-ecological models of the evolution of pesticide resistance under different types of crop rotation and pesticide application regimes.

Maintained by A. Bradley Duthie. Last updated 1 years ago.

26.4 match 3 stars 4.65 score 1 scripts

trevorld

ggpattern:'ggplot2' Pattern Geoms

Provides 'ggplot2' geoms filled with various patterns. Includes a patterned version of every 'ggplot2' geom that has a region that can be filled with a pattern. Provides a suite of 'ggplot2' aesthetics and scales for controlling pattern appearances. Supports over a dozen builtin patterns (every pattern implemented by 'gridpattern') as well as allowing custom user-defined patterns.

Maintained by Trevor L. Davis. Last updated 2 months ago.

9.9 match 368 stars 12.33 score 1.7k scripts 3 dependents

epiverse-trace

ColOpenData:Download Colombian Demographic, Climate and Geospatial Data

Downloads wrangled Colombian socioeconomic, geospatial,population and climate data from DANE <https://www.dane.gov.co/> (National Administrative Department of Statistics) and IDEAM <https://ideam.gov.co> (Institute of Hydrology, Meteorology and Environmental Studies). It solves the problem of Colombian data being issued in different web pages and sources by using functions that allow the user to select the desired database and download it without having to do the exhausting acquisition process.

Maintained by Maria Camila Tavera-Cifuentes. Last updated 1 months ago.

climate colombia data-package demographics maps

16.2 match 11 stars 7.44 score 17 scripts

r-lib

lintr:A 'Linter' for R Code

Checks adherence to a given style, syntax errors and possible semantic issues. Supports on the fly checking of R code edited with 'RStudio IDE', 'Emacs', 'Vim', 'Sublime Text', 'Atom' and 'Visual Studio Code'.

Maintained by Michael Chirico. Last updated 8 days ago.

linter

7.1 match 1.2k stars 17.00 score 916 scripts 33 dependents

markbravington

mvbutils:General utilities, workspace organization, code and docu editing, live package maintenance, etc

Hierarchical workspace tree, code editing and backup, easy package prep, editing of packages while loaded, per-object lazy-loading, easy documentation, macro functions, and miscellaneous utilities. Needed by debug package.

Maintained by Mark V. Bravington. Last updated 6 days ago.

18.5 match 6.53 score 138 scripts 18 dependents

mschubert

narray:Subset- And Name-Aware Array Utility Functions

Stacking arrays according to dimension names, subset-aware splitting and mapping of functions, intersecting along arbitrary dimensions, converting to and from data.frames, and many other helper functions.

Maintained by Michael Schubert. Last updated 2 months ago.

array utility cpp

17.5 match 27 stars 6.91 score 10 scripts 10 dependents

mlr-org

mlr3misc:Helper Functions for 'mlr3'

Frequently used helper functions and assertions used in 'mlr3' and its companion packages. Comes with helper functions for functional programming, for printing, to work with 'data.table', as well as some generally useful 'R6' classes. This package also supersedes the package 'BBmisc'.

Maintained by Marc Becker. Last updated 4 months ago.

machine-learning miscellaneous mlr3

11.7 match 12 stars 10.28 score 302 scripts 42 dependents

lindbrook

cholera:Amend, Augment and Aid Analysis of John Snow's Cholera Map

Amends errors, augments data and aids analysis of John Snow's map of the 1854 London cholera outbreak.

Maintained by lindbrook. Last updated 23 hours ago.

cholera data-visualization datasets epidemiology john-snow public-health triangulation-delaunay voronoi voronoi-polygons

12.7 match 136 stars 9.33 score 95 scripts

trinker

textshape:Tools for Reshaping Text

Tools that can be used to reshape and restructure text data.

Maintained by Tyler Rinker. Last updated 12 months ago.

data-reshaping manipulation sentence-boundary-detection text-data text-formating tidy

12.9 match 50 stars 9.18 score 266 scripts 34 dependents

tdhock

nc:Named Capture to Data Tables

User-friendly functions for extracting a data table (row for each match, column for each group) from non-tabular text data using regular expressions, and for melting columns that match a regular expression. Patterns are defined using a readable syntax that makes it easy to build complex patterns in terms of simpler, re-usable sub-patterns. Named R arguments are translated to column names in the output; capture groups without names are used internally in order to provide a standard interface to three regular expression 'C' libraries ('PCRE', 'RE2', 'ICU'). Output can also include numeric columns via user-specified type conversion functions.

Maintained by Toby Hocking. Last updated 2 months ago.

17.3 match 16 stars 6.85 score 46 scripts

janmarvin

openxlsx2:Read, Write and Edit 'xlsx' Files

Simplifies the creation of 'xlsx' files by providing a high level interface to writing, styling and editing worksheets.

Maintained by Jan Marvin Garbuszus. Last updated 1 days ago.

xlsx cpp

8.6 match 138 stars 13.67 score 194 scripts 11 dependents

snystrom

cmdfun:Framework for Building Interfaces to Shell Commands

Writing interfaces to command line software is cumbersome. 'cmdfun' provides a framework for building function calls to seamlessly interface with shell commands by allowing lazy evaluation of command line arguments. 'cmdfun' also provides methods for handling user-specific paths to tool installs or secrets like API keys. Its focus is to equally serve package builders who wish to wrap command line software, and to help analysts stay inside R when they might usually leave to execute non-R software.

Maintained by Spencer Nystrom. Last updated 4 years ago.

19.4 match 15 stars 6.05 score 7 scripts 5 dependents

andysouth

rworldmap:Mapping Global Data

Enables mapping of country level and gridded user datasets.

Maintained by Andy South. Last updated 2 years ago.

9.9 match 30 stars 11.83 score 3.2k scripts 14 dependents

bioc

GenomeInfoDb:Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.

Maintained by Hervé Pagès. Last updated 2 months ago.

genetics datarepresentation annotation genomeannotation bioconductor-package core-package

7.1 match 32 stars 16.46 score 1.3k scripts 1.7k dependents

trevorld

xmpdf:Edit 'XMP' Metadata and 'PDF' Bookmarks and Documentation Info

Edit 'XMP' metadata <https://en.wikipedia.org/wiki/Extensible_Metadata_Platform> in a variety of media file formats as well as edit bookmarks (aka outline aka table of contents) and documentation info entries in 'pdf' files. Can detect and use a variety of command-line tools to perform these operations such as 'exiftool' <https://exiftool.org/>, 'ghostscript' <https://www.ghostscript.com/>, and/or 'pdftk' <https://gitlab.com/pdftk-java/pdftk>.

Maintained by Trevor L Davis. Last updated 12 months ago.

22.6 match 5 stars 5.18 score 1 scripts 1 dependents

bioc

flowWorkspace:Infrastructure for representing and interacting with gated and ungated cytometry data sets.

This package is designed to facilitate comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.

Maintained by Greg Finak. Last updated 10 days ago.

immunooncology flowcytometry dataimport preprocessing datarepresentation zlib openblas cpp

14.8 match 7.89 score 576 scripts 10 dependents

r-lib

vctrs:Vector Helpers

Defines new notions of prototype and size that are used to provide tools for consistent and well-founded type-coercion and size-recycling, and are in turn connected to ideas of type- and size-stability useful for analysing function interfaces.

Maintained by Davis Vaughan. Last updated 5 months ago.

s3-vectors

6.1 match 290 stars 18.97 score 1.1k scripts 13k dependents

klmr

box:Write Reusable, Composable and Modular R Code

A modern module system for R. Organise code into hierarchical, composable, reusable modules, and use it effortlessly across projects via a flexible, declarative dependency loading syntax.

Maintained by Konrad Rudolph. Last updated 12 days ago.

modules packages

9.3 match 888 stars 12.39 score 47 scripts 4 dependents

mine-cetinkaya-rundel

ukbabynames:UK Baby Names Data

Full listing of UK baby names occurring more than three times per year between 1974 and 2020, and rankings of baby name popularity by decade from 1904 to 1994.

Maintained by Mine Çetinkaya-Rundel. Last updated 3 years ago.

data opendata uk

22.9 match 21 stars 5.03 score 34 scripts

trinker

wakefield:Generate Random Data Sets

Generates random data sets including: data.frames, lists, and vectors.

Maintained by Tyler Rinker. Last updated 5 years ago.

data-generation wakefield

16.1 match 256 stars 7.13 score 209 scripts

ropensci

phruta:Phylogenetic Reconstruction and Time-dating

The phruta R package is designed to simplify the basic phylogenetic pipeline. Specifically, all code is run within the same program and data from intermediate steps are saved in independent folders. Furthermore, all code is run within the same environment which increases the reproducibility of your analysis. phruta retrieves gene sequences, combines newly downloaded and local gene sequences, and performs sequence alignments.

Maintained by Cristian Roman Palacios. Last updated 8 months ago.

24.2 match 9 stars 4.75 score 14 scripts

bioc

seqsetvis:Set Based Visualizations for Next-Gen Sequencing Data

seqsetvis enables the visualization and analysis of sets of genomic sites in next gen sequencing data. Although seqsetvis was designed for the comparison of mulitple ChIP-seq samples, this package is domain-agnostic and allows the processing of multiple genomic coordinate files (bed-like files) and signal files (bigwig files pileups from bam file). seqsetvis has multiple functions for fetching data from regions into a tidy format for analysis in data.table or tidyverse and visualization via ggplot2.

Maintained by Joseph R Boyd. Last updated 3 months ago.

software chipseq multiplecomparison sequencing visualization

19.7 match 5.82 score 82 scripts

bioc

rhdf5:R Interface to HDF5

This package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.

Maintained by Mike Smith. Last updated 2 months ago.

infrastructure dataimport hdf5 rhdf5 openssl curl zlib cpp

7.2 match 62 stars 15.93 score 4.2k scripts 232 dependents

rich-iannone

DiagrammeR:Graph/Network Visualization

Build graph/network structures using functions for stepwise addition and deletion of nodes and edges. Work with data available in tables for bulk addition of nodes, edges, and associated metadata. Use graph selections and traversals to apply changes to specific nodes or edges. A wide selection of graph algorithms allow for the analysis of graphs. Visualize the graphs and take advantage of any aesthetic properties assigned to nodes and edges.

Maintained by Richard Iannone. Last updated 2 months ago.

graph graph-functions network-graph property-graph visualization

7.5 match 1.7k stars 15.18 score 3.8k scripts 87 dependents

jamiemkass

ENMeval:Automated Tuning and Evaluations of Ecological Niche Models

Runs ecological niche models over all combinations of user-defined settings (i.e., tuning), performs cross validation to evaluate models, and returns data tables to aid in selection of optimal model settings that balance goodness-of-fit and model complexity. Also has functions to partition data spatially (or not) for cross validation, to plot multiple visualizations of results, to run null models to estimate significance and effect sizes of performance metrics, and to calculate range overlap between model predictions, among others. The package was originally built for Maxent models (Phillips et al. 2006, Phillips et al. 2017), but the current version allows possible extensions for any modeling algorithm. The extensive vignette, which guides users through most package functionality but unfortunately has a file size too big for CRAN, can be found here on the package's Github Pages website: <https://jamiemkass.github.io/ENMeval/articles/ENMeval-2.0-vignette.html>.

Maintained by Jamie M. Kass. Last updated 2 months ago.

10.1 match 49 stars 11.25 score 332 scripts 2 dependents

melff

memisc:Management of Survey Data and Presentation of Analysis Results

An infrastructure for the management of survey data including value labels, definable missing values, recoding of variables, production of code books, and import of (subsets of) 'SPSS' and 'Stata' files is provided. Further, the package allows to produce tables and data frames of arbitrary descriptive statistics and (almost) publication-ready tables of regression model estimates, which can be exported to 'LaTeX' and HTML.

Maintained by Martin Elff. Last updated 11 days ago.

survey-data

9.1 match 46 stars 12.34 score 1.2k scripts 13 dependents

gdemin

expss:Tables, Labels and Some Useful Functions from Spreadsheets and 'SPSS' Statistics

Package computes and displays tables with support for 'SPSS'-style labels, multiple and nested banners, weights, multiple-response variables and significance testing. There are facilities for nice output of tables in 'knitr', 'Shiny', '*.xlsx' files, R and 'Jupyter' notebooks. Methods for labelled variables add value labels support to base R functions and to some functions from other packages. Additionally, the package brings popular data transformation functions from 'SPSS' Statistics and 'Excel': 'RECODE', 'COUNT', 'COUNTIF', 'VLOOKUP' and etc. These functions are very useful for data processing in marketing research surveys. Package intended to help people to move data processing from 'Excel' and 'SPSS' to R.

Maintained by Gregory Demin. Last updated 11 months ago.

excel labels labels-support msexcel pivot-tables recode spss spss-statistics tables variable-labels vlookup

10.2 match 84 stars 11.00 score 1.8k scripts 4 dependents

ropensci

stats19:Work with Open Road Traffic Casualty Data from Great Britain

Tools to help download, process and analyse the UK road collision data collected using the 'STATS19' form. The datasets are provided as 'CSV' files with detailed road safety information about the circumstances of car crashes and other incidents on the roads resulting in casualties in Great Britain from 1979 to present. Tables are available on 'colissions' with the circumstances (e.g. speed limit of road), information about 'vehicles' involved (e.g. type of vehicle), and 'casualties' (e.g. age). The statistics relate only to events on public roads that were reported to the police, and subsequently recorded, using the 'STATS19' collision reporting form. See the Department for Transport website <https://www.data.gov.uk/dataset/cb7ae6f0-4be6-4935-9277-47e5ce24a11f/road-accidents-safety-data> for more information on these datasets. The package is described in a paper in the Journal of Open Source Software (Lovelace et al. 2019) <doi:10.21105/joss.01181>. See Gilardi et al. (2022) <doi:10.1111/rssa.12823>, Vidal-Tortosa et al. (2021) <doi:10.1016/j.jth.2021.101291>, and Tait et al. (2023) <doi:10.1016/j.aap.2022.106895> for examples of how the data can be used for methodological and empirical road safety research.

Maintained by Robin Lovelace. Last updated 2 months ago.

stats19 road-safety transport car-crashes ropensci data

12.1 match 64 stars 9.20 score 193 scripts

bioc

BUSpaRse:kallisto | bustools R utilities

The kallisto | bustools pipeline is a fast and modular set of tools to convert single cell RNA-seq reads in fastq files into gene count or transcript compatibility counts (TCC) matrices for downstream analysis. Central to this pipeline is the barcode, UMI, and set (BUS) file format. This package serves the following purposes: First, this package allows users to manipulate BUS format files as data frames in R and then convert them into gene count or TCC matrices. Furthermore, since R and Rcpp code is easier to handle than pure C++ code, users are encouraged to tweak the source code of this package to experiment with new uses of BUS format and different ways to convert the BUS file into gene count matrix. Second, this package can conveniently generate files required to generate gene count matrices for spliced and unspliced transcripts for RNA velocity. Here biotypes can be filtered and scaffolds and haplotypes can be removed, and the filtered transcriptome can be extracted and written to disk. Third, this package implements utility functions to get transcripts and associated genes required to convert BUS files to gene count matrices, to write the transcript to gene information in the format required by bustools, and to read output of bustools into R as sparses matrices.

Maintained by Lambda Moses. Last updated 5 months ago.

singlecell rnaseq workflowstep cpp

15.0 match 9 stars 7.35 score 165 scripts

bergsmat

nonmemica:Create and Evaluate NONMEM Models in a Project Context

Systematically creates and modifies NONMEM(R) control streams. Harvests NONMEM output, builds run logs, creates derivative data, generates diagnostics. NONMEM (ICON Development Solutions <https://www.iconplc.com/>) is software for nonlinear mixed effects modeling. See 'package?nonmemica'.

Maintained by Tim Bergsma. Last updated 2 months ago.

24.1 match 4 stars 4.58 score 45 scripts

rich-iannone

i18n:Internationalization Data from the 'Unicode CLDR' in Tabular Form

Up-to-date data from the 'Unicode CLDR Project' (where 'CLDR' stands for 'Common Locale Data Repository') are available here as a series of easy-to-parse datasets. Several functions are provided for extracting key elements from the tabular datasets.

Maintained by Richard Iannone. Last updated 9 months ago.

29.8 match 10 stars 3.70 score 9 scripts

talgalili

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

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

Maintained by Tal Galili. Last updated 1 years ago.

10.8 match 273 stars 10.19 score 1.2k scripts

ropensci

targets:Dynamic Function-Oriented 'Make'-Like Declarative Pipelines

Pipeline tools coordinate the pieces of computationally demanding analysis projects. The 'targets' package is a 'Make'-like pipeline tool for statistics and data science in R. The package skips costly runtime for tasks that are already up to date, orchestrates the necessary computation with implicit parallel computing, and abstracts files as R objects. If all the current output matches the current upstream code and data, then the whole pipeline is up to date, and the results are more trustworthy than otherwise. The methodology in this package borrows from GNU 'Make' (2015, ISBN:978-9881443519) and 'drake' (2018, <doi:10.21105/joss.00550>).

Maintained by William Michael Landau. Last updated 2 days ago.

data-science high-performance-computing make peer-reviewed pipeline r-targetopia reproducibility reproducible-research targets workflow

7.2 match 973 stars 15.20 score 4.6k scripts 22 dependents

ropensci

antanym:Antarctic Geographic Place Names

Antarctic geographic names from the Composite Gazetteer of Antarctica, and functions for working with those place names.

Maintained by Ben Raymond. Last updated 3 years ago.

antarctic southern ocean place names gazetteer peer-reviewed

28.1 match 7 stars 3.89 score 22 scripts

flr

FLCore:Core Package of FLR, Fisheries Modelling in R

Core classes and methods for FLR, a framework for fisheries modelling and management strategy simulation in R. Developed by a team of fisheries scientists in various countries. More information can be found at <http://flr-project.org/>.

Maintained by Iago Mosqueira. Last updated 9 days ago.

fisheries flr fisheries-modelling

12.4 match 16 stars 8.78 score 956 scripts 23 dependents

statnet

statnet.common:Common R Scripts and Utilities Used by the Statnet Project Software

Non-statistical utilities used by the software developed by the Statnet Project. They may also be of use to others.

Maintained by Pavel N. Krivitsky. Last updated 26 days ago.

9.5 match 8 stars 11.42 score 197 scripts 148 dependents

gustavobio

flora:Tools for Interacting with the Brazilian Flora 2020

Tools to quickly compile taxonomic and distribution data from the Brazilian Flora 2020.

Maintained by Gustavo Carvalho. Last updated 1 years ago.

20.2 match 29 stars 5.37 score 54 scripts 1 dependents

bioc

MOFA2:Multi-Omics Factor Analysis v2

The MOFA2 package contains a collection of tools for training and analysing multi-omic factor analysis (MOFA). MOFA is a probabilistic factor model that aims to identify principal axes of variation from data sets that can comprise multiple omic layers and/or groups of samples. Additional time or space information on the samples can be incorporated using the MEFISTO framework, which is part of MOFA2. Downstream analysis functions to inspect molecular features underlying each factor, vizualisation, imputation etc are available.

Maintained by Ricard Argelaguet. Last updated 5 months ago.

dimensionreduction bayesian visualization factor-analysis mofa multi-omics

10.8 match 319 stars 10.02 score 502 scripts

cardiomoon

ztable:Zebra-Striped Tables in LaTeX and HTML Formats

Makes zebra-striped tables (tables with alternating row colors) in LaTeX and HTML formats easily from a data.frame, matrix, lm, aov, anova, glm, coxph, nls, fitdistr, mytable and cbind.mytable objects.

Maintained by Keon-Woong Moon. Last updated 2 years ago.

13.7 match 21 stars 7.90 score 212 scripts 2 dependents

tanaylab

misha:Toolkit for Analysis of Genomic Data

A toolkit for analysis of genomic data. The 'misha' package implements an efficient data structure for storing genomic data, and provides a set of functions for data extraction, manipulation and analysis. Some of the 2D genome algorithms were described in Yaffe and Tanay (2011) <doi:10.1038/ng.947>.

Maintained by Aviezer Lifshitz. Last updated 5 days ago.

genomic-data-analysis cpp

18.4 match 4 stars 5.86 score

qile0317

FastUtils:Fast, Readable Utility Functions

A wide variety of tools for general data analysis, wrangling, spelling, statistics, visualizations, package development, and more. All functions have vectorized implementations whenever possible. Exported names are designed to be readable, with longer names possessing short aliases.

Maintained by Qile Yang. Last updated 4 months ago.

scientific-computing utilities utility cpp

21.7 match 2 stars 4.95 score 2 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.

geomorphometry geoprocessing geospatial gis hydrology remote-sensing rstudio

11.1 match 173 stars 9.65 score 203 scripts 2 dependents

framverse

framrsquared:FRAM Database Interface

A convenient tool for interfacing with FRAM access databases in R environments.

Maintained by Ty Garber. Last updated 2 months ago.

21.1 match 6 stars 5.06 score 9 scripts

jl5000

tidyged:Handle GEDCOM Files Using Tidyverse Principles

Create and summarise family tree GEDCOM files using tidy dataframes.

Maintained by Jamie Lendrum. Last updated 3 years ago.

17.8 match 8 stars 5.96 score 23 scripts 3 dependents

bioc

cola:A Framework for Consensus Partitioning

Subgroup classification is a basic task in genomic data analysis, especially for gene expression and DNA methylation data analysis. It can also be used to test the agreement to known clinical annotations, or to test whether there exist significant batch effects. The cola package provides a general framework for subgroup classification by consensus partitioning. It has the following features: 1. It modularizes the consensus partitioning processes that various methods can be easily integrated. 2. It provides rich visualizations for interpreting the results. 3. It allows running multiple methods at the same time and provides functionalities to straightforward compare results. 4. It provides a new method to extract features which are more efficient to separate subgroups. 5. It automatically generates detailed reports for the complete analysis. 6. It allows applying consensus partitioning in a hierarchical manner.

Maintained by Zuguang Gu. Last updated 1 months ago.

clustering geneexpression classification software consensus-clustering cpp

14.0 match 61 stars 7.49 score 112 scripts

hzhanghenry

RCircos:Circos 2D Track Plot

A simple and flexible way to generate Circos 2D track plot images for genomic data visualization is implemented in this package. The types of plots include: heatmap, histogram, lines, scatterplot, tiles and plot items for further decorations include connector, link (lines and ribbons), and text (gene) label. All functions require only R graphics package that comes with R base installation.

Maintained by Hongen Zhang. Last updated 3 years ago.

14.5 match 6 stars 7.21 score 298 scripts 3 dependents

ddalthorp

dwp:Density-Weighted Proportion

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

Maintained by Daniel Dalthorp. Last updated 2 years ago.

38.6 match 1 stars 2.70 score

fbellelli

countries:Deal with Country Data in an Easy Way

Wrangle country data more effectively and quickly. This package contains functions to easily identify and convert country names, download country information, merge country data from different sources, and make quick world maps.

Maintained by Francesco Saverio Bellelli. Last updated 22 days ago.

20.2 match 3 stars 5.15 score 47 scripts

tidyverse

tibble:Simple Data Frames

Provides a 'tbl_df' class (the 'tibble') with stricter checking and better formatting than the traditional data frame.

Maintained by Kirill Müller. Last updated 3 months ago.

tidy-data

4.5 match 693 stars 22.82 score 47k scripts 11k dependents

bioc

aCGH:Classes and functions for Array Comparative Genomic Hybridization data

Functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects.

Maintained by Peter Dimitrov. Last updated 5 months ago.

copynumbervariation dataimport genetics cpp

19.3 match 5.38 score 9 scripts 4 dependents

cbielow

PTXQC:Quality Report Generation for MaxQuant and mzTab Results

Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the MaxQuant software suite (from .txt files) or mzTab files (ideally from OpenMS 'QualityControl' tool). Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format. Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015) <doi:10.1021/acs.jproteome.5b00780>.

Maintained by Chris Bielow. Last updated 1 years ago.

drag-and-drop hacktoberfest heatmap match-between-runs maxquant metric mztab openms proteomics quality-control quality-metrics report

11.1 match 42 stars 9.35 score 105 scripts 1 dependents

skranz

gtree:gtree basic functionality to model and solve games

gtree basic functionality to model and solve games

Maintained by Sebastian Kranz. Last updated 4 years ago.

economic-experiments economics gambit game-theory nash-equilibrium

27.2 match 18 stars 3.79 score 23 scripts 1 dependents

matthiaspucher

staRdom:PARAFAC Analysis of EEMs from DOM

'This is a user-friendly way to run a parallel factor (PARAFAC) analysis (Harshman, 1971) <doi:10.1121/1.1977523> on excitation emission matrix (EEM) data from dissolved organic matter (DOM) samples (Murphy et al., 2013) <doi:10.1039/c3ay41160e>. The analysis includes profound methods for model validation. Some additional functions allow the calculation of absorbance slope parameters and create beautiful plots.'

Maintained by Matthias Pucher. Last updated 4 months ago.

17.0 match 21 stars 6.03 score 86 scripts

calvagone

campsismod:Generic Implementation of a PK/PD Model

A generic, easy-to-use and expandable implementation of a pharmacokinetic (PK) / pharmacodynamic (PD) model based on the S4 class system. This package allows the user to read/write a pharmacometric model from/to files and adapt it further on the fly in the R environment. For this purpose, this package provides an intuitive API to add, modify or delete equations, ordinary differential equations (ODE's), model parameters or compartment properties (like infusion duration or rate, bioavailability and initial values). Finally, this package also provides a useful export of the model for use with simulation packages 'rxode2' and 'mrgsolve'. This package is designed and intended to be used with package 'campsis', a PK/PD simulation platform built on top of 'rxode2' and 'mrgsolve'.

Maintained by Nicolas Luyckx. Last updated 1 months ago.

15.5 match 5 stars 6.64 score 42 scripts 1 dependents

bbuchsbaum

neuroim:Data Structures and Handling for Neuroimaging Data

A collection of data structures that represent volumetric brain imaging data. The focus is on basic data handling for 3D and 4D neuroimaging data. In addition, there are function to read and write NIFTI files and limited support for reading AFNI files.

Maintained by Bradley Buchsbaum. Last updated 4 years ago.

cpp

18.2 match 6 stars 5.64 score 48 scripts

ropensci

refsplitr:author name disambiguation, author georeferencing, and mapping of coauthorship networks with 'Web of Science' data

Tools to parse and organize reference records downloaded from the 'Web of Science' citation database into an R-friendly format, disambiguate the names of authors, geocode their locations, and generate/visualize coauthorship networks. This package has been peer-reviewed by rOpenSci (v. 1.0).

Maintained by Emilio Bruna. Last updated 7 months ago.

name disambiguation bibliometrics coauthorship collaboration georeferencing metascience references scientometrics science of science web of science

18.1 match 55 stars 5.64 score 16 scripts

parklab

Nozzle.R1:Nozzle Reports

The Nozzle package provides an API to generate HTML reports with dynamic user interface elements based on JavaScript and CSS (Cascading Style Sheets). Nozzle was designed to facilitate summarization and rapid browsing of complex results in data analysis pipelines where multiple analyses are performed frequently on big data sets. The package can be applied to any project where user-friendly reports need to be created.

Maintained by Nils Gehlenborg. Last updated 10 years ago.

gehlenborglab html-report reproducible-research

19.0 match 68 stars 5.31 score 10 scripts 2 dependents

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 5 days ago.

exonarray geneexpression transcription alternativesplicing differentialexpression differentialsplicing genesetenrichment dataimport bayesian clustering regression timecourse microarray micrornaarray mrnamicroarray onechannel proprietaryplatforms twochannel sequencing rnaseq batcheffect multiplecomparison normalization preprocessing qualitycontrol biomedicalinformatics cellbiology cheminformatics epigenetics functionalgenomics genetics immunooncology metabolomics proteomics systemsbiology transcriptomics

7.3 match 13.81 score 16k scripts 585 dependents

idem-lab

conmat:Builds Contact Matrices using GAMs and Population Data

Builds contact matrices using GAMs and population data. This package incorporates data that is copyright Commonwealth of Australia (Australian Electoral Commission and Australian Bureau of Statistics) 2020.

Maintained by Nicholas Tierney. Last updated 7 days ago.

contact-matrices infectious-diseases population-data public-health

13.8 match 19 stars 7.21 score 47 scripts

poissonconsulting

nlist:Lists of Numeric Atomic Objects

Create and manipulate numeric list ('nlist') objects. An 'nlist' is an S3 list of uniquely named numeric objects. An numeric object is an integer or double vector, matrix or array. An 'nlists' object is a S3 class list of 'nlist' objects with the same names, dimensionalities and typeofs. Numeric list objects are of interest because they are the raw data inputs for analytic engines such as 'JAGS', 'STAN' and 'TMB'. Numeric lists objects, which are useful for storing multiple realizations of of simulated data sets, can be converted to coda::mcmc and coda::mcmc.list objects.

Maintained by Joe Thorley. Last updated 2 months ago.

data-frame natomic nlist nlists

13.8 match 6 stars 7.23 score 13 scripts 12 dependents

alphaprime7

normfluodbf:Cleans and Normalizes FLUOstar DBF and DAT Files from 'Liposome' Flux Assays

Cleans and Normalizes FLUOstar DBF and DAT Files obtained from liposome flux assays. Users should verify extended usage of the package on files from other assay types.

Maintained by Tingwei Adeck. Last updated 4 months ago.

19.9 match 1 stars 4.98 score 12 scripts

jacobkap

predictrace:Predict the Race and Gender of a Given Name Using Census and Social Security Administration Data

Predicts the most common race of a surname and based on U.S. Census data, and the most common first named based on U.S. Social Security Administration data.

Maintained by Jacob Kaplan. Last updated 2 years ago.

19.7 match 12 stars 5.03 score 18 scripts

pik-piam

magclass:Data Class and Tools for Handling Spatial-Temporal Data

Data class for increased interoperability working with spatial-temporal data together with corresponding functions and methods (conversions, basic calculations and basic data manipulation). The class distinguishes between spatial, temporal and other dimensions to facilitate the development and interoperability of tools build for it. Additional features are name-based addressing of data and internal consistency checks (e.g. checking for the right data order in calculations).

Maintained by Jan Philipp Dietrich. Last updated 10 days ago.

8.8 match 5 stars 11.16 score 412 scripts 56 dependents

ropensci

redland:RDF Library Bindings in R

Provides methods to parse, query and serialize information stored in the Resource Description Framework (RDF). RDF is described at <https://www.w3.org/TR/rdf-primer/>. This package supports RDF by implementing an R interface to the Redland RDF C library, described at <https://librdf.org/docs/api/index.html>. In brief, RDF provides a structured graph consisting of Statements composed of Subject, Predicate, and Object Nodes.

Maintained by Matthew B. Jones. Last updated 1 years ago.

redland

12.5 match 17 stars 7.85 score 98 scripts 13 dependents

daattali

ddpcr:Analysis and Visualization of Droplet Digital PCR in R and on the Web

An interface to explore, analyze, and visualize droplet digital PCR (ddPCR) data in R. This is the first non-proprietary software for analyzing two-channel ddPCR data. An interactive tool was also created and is available online to facilitate this analysis for anyone who is not comfortable with using R.

Maintained by Dean Attali. Last updated 12 months ago.

10.3 match 61 stars 9.54 score 131 scripts 2 dependents

ncss-tech

SoilTaxonomy:A System of Soil Classification for Making and Interpreting Soil Surveys

Taxonomic dictionaries, formative element lists, and functions related to the maintenance, development and application of U.S. Soil Taxonomy. Data and functionality are based on official U.S. Department of Agriculture sources including the latest edition of the Keys to Soil Taxonomy. Descriptions and metadata are obtained from the National Soil Information System or Soil Survey Geographic databases. Other sources are referenced in the data documentation. Provides tools for understanding and interacting with concepts in the U.S. Soil Taxonomic System. Most of the current utilities are for working with taxonomic concepts at the "higher" taxonomic levels: Order, Suborder, Great Group, and Subgroup.

Maintained by Andrew Brown. Last updated 6 months ago.

great-group ncss-tech soil soil-survey soil-taxonomy subgroup suborder usda

17.3 match 15 stars 5.65 score

metrumresearchgroup

mrgsolve:Simulate from ODE-Based Models

Fast simulation from ordinary differential equation (ODE) based models typically employed in quantitative pharmacology and systems biology.

Maintained by Kyle T Baron. Last updated 1 months ago.

mrgsolve ode openblas cpp

8.9 match 138 stars 10.90 score 1.2k scripts 3 dependents

bioc

KEGGgraph:KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor

KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc.

Maintained by Jitao David Zhang. Last updated 5 months ago.

pathways graphandnetwork visualization kegg

12.4 match 7.76 score 114 scripts 23 dependents

aphalo

photobiology:Photobiological Calculations

Definitions of classes, methods, operators and functions for use in photobiology and radiation meteorology and climatology. Calculation of effective (weighted) and not-weighted irradiances/doses, fluence rates, transmittance, reflectance, absorptance, absorbance and diverse ratios and other derived quantities from spectral data. Local maxima and minima: peaks, valleys and spikes. Conversion between energy-and photon-based units. Wavelength interpolation. Astronomical calculations related solar angles and day length. Colours and vision. This package is part of the 'r4photobiology' suite, Aphalo, P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.

Maintained by Pedro J. Aphalo. Last updated 3 days ago.

light photobiology quantification r4photobiology-suite radiation spectra sun-position

10.3 match 4 stars 9.35 score 604 scripts 12 dependents

spatstat

spatstat.utils:Utility Functions for 'spatstat'

Contains utility functions for the 'spatstat' family of packages which may also be useful for other purposes.

Maintained by Adrian Baddeley. Last updated 2 days ago.

spatial-analysis spatial-data spatstat

8.3 match 5 stars 11.66 score 134 scripts 248 dependents

helixcn

phylotools:Phylogenetic Tools for Eco-Phylogenetics

A collection of tools for building RAxML supermatrix using PHYLIP or aligned FASTA files. These functions will be useful for building large phylogenies using multiple markers.

Maintained by Jinlong Zhang. Last updated 5 months ago.

13.1 match 11 stars 7.31 score 368 scripts

rudeboybert

fivethirtyeight:Data and Code Behind the Stories and Interactives at 'FiveThirtyEight'

Datasets and code published by the data journalism website 'FiveThirtyEight' available at <https://github.com/fivethirtyeight/data>. Note that while we received guidance from editors at 'FiveThirtyEight', this package is not officially published by 'FiveThirtyEight'.

Maintained by Albert Y. Kim. Last updated 2 years ago.

data-science datajournalism fivethirtyeight statistics

8.7 match 453 stars 10.98 score 1.7k scripts

r-lib

whoami:Username, Full Name, Email Address, 'GitHub' Username of the Current User

Look up the username and full name of the current user, the current user's email address and 'GitHub' username, using various sources of system and configuration information.

Maintained by Gábor Csárdi. Last updated 5 months ago.

10.1 match 19 stars 9.48 score 36 scripts 39 dependents

ctn-0094

DOPE:Drug Ontology Parsing Engine

Provides information on drug names (brand, generic and street) for drugs tracked by the DEA. There are functions that will search synonyms and return the drug names and types. The vignettes have extensive information on the work done to create the data for the package.

Maintained by Raymond Balise. Last updated 4 years ago.

12.2 match 21 stars 7.83 score 31 scripts

poissonconsulting

chk:Check User-Supplied Function Arguments

For developers to check user-supplied function arguments. It is designed to be simple, fast and customizable. Error messages follow the tidyverse style guide.

Maintained by Joe Thorley. Last updated 2 months ago.

chk

8.0 match 48 stars 11.89 score 22 scripts 95 dependents

sticsrpacks

SticsRFiles:Read and Modify 'STICS' Input/Output Files

Manipulating input and output files of the 'STICS' crop model. Files are either 'JavaSTICS' XML files or text files used by the model 'fortran' executable. Most basic functionalities are reading or writing parameter names and values in both XML or text input files, and getting data from output files. Advanced functionalities include XML files generation from XML templates and/or spreadsheets, or text files generation from XML files by using 'xslt' transformation.

Maintained by Patrice Lecharpentier. Last updated 18 days ago.

11.5 match 4 stars 8.27 score 124 scripts

mllg

checkmate:Fast and Versatile Argument Checks

Tests and assertions to perform frequent argument checks. A substantial part of the package was written in C to minimize any worries about execution time overhead.

Maintained by Michel Lang. Last updated 8 months ago.

assertions testthat

5.8 match 276 stars 16.28 score 1.5k scripts 1.9k dependents

bioc

philr:Phylogenetic partitioning based ILR transform for metagenomics data

PhILR is short for Phylogenetic Isometric Log-Ratio Transform. This package provides functions for the analysis of compositional data (e.g., data representing proportions of different variables/parts). Specifically this package allows analysis of compositional data where the parts can be related through a phylogenetic tree (as is common in microbiota survey data) and makes available the Isometric Log Ratio transform built from the phylogenetic tree and utilizing a weighted reference measure.

Maintained by Justin Silverman. Last updated 5 months ago.

immunooncology sequencing microbiome metagenomics software

11.8 match 19 stars 7.99 score 95 scripts

debruine

faux:Simulation for Factorial Designs

Create datasets with factorial structure through simulation by specifying variable parameters. Extended documentation at <https://debruine.github.io/faux/>. Described in DeBruine (2020) <doi:10.5281/zenodo.2669586>.

Maintained by Lisa DeBruine. Last updated 2 months ago.

data simulation

10.1 match 98 stars 9.35 score 716 scripts 1 dependents

bioc

ballgown:Flexible, isoform-level differential expression analysis

Tools for statistical analysis of assembled transcriptomes, including flexible differential expression analysis, visualization of transcript structures, and matching of assembled transcripts to annotation.

Maintained by Jack Fu. Last updated 5 months ago.

immunooncology rnaseq statisticalmethod preprocessing differentialexpression

8.9 match 146 stars 10.51 score 338 scripts 1 dependents

rstudio

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.

6.9 match 845 stars 13.57 score 264 scripts 2 dependents

hadley

plyr:Tools for Splitting, Applying and Combining Data

A set of tools that solves a common set of problems: you need to break a big problem down into manageable pieces, operate on each piece and then put all the pieces back together. For example, you might want to fit a model to each spatial location or time point in your study, summarise data by panels or collapse high-dimensional arrays to simpler summary statistics. The development of 'plyr' has been generously supported by 'Becton Dickinson'.

Maintained by Hadley Wickham. Last updated 4 months ago.

cpp

5.2 match 500 stars 18.16 score 83k scripts 3.3k dependents

jokergoo

circlize:Circular Visualization

Circular layout is an efficient way for the visualization of huge amounts of information. Here this package provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of the package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, it gives users more convenience and freedom to design figures for better understanding complex patterns behind multiple dimensional data. The package is described in Gu et al. 2014 <doi:10.1093/bioinformatics/btu393>.

Maintained by Zuguang Gu. Last updated 1 years ago.

5.9 match 983 stars 15.62 score 10k scripts 213 dependents

philips-software

latrend:A Framework for Clustering Longitudinal Data

A framework for clustering longitudinal datasets in a standardized way. The package provides an interface to existing R packages for clustering longitudinal univariate trajectories, facilitating reproducible and transparent analyses. Additionally, standard tools are provided to support cluster analyses, including repeated estimation, model validation, and model assessment. The interface enables users to compare results between methods, and to implement and evaluate new methods with ease. The 'akmedoids' package is available from <https://github.com/MAnalytics/akmedoids>.

Maintained by Niek Den Teuling. Last updated 2 months ago.

cluster-analysis clustering-evaluation clustering-methods data-science longitudinal-clustering longitudinal-data mixture-models time-series-analysis

13.6 match 30 stars 6.77 score 26 scripts

gluc

data.tree:General Purpose Hierarchical Data Structure

Create tree structures from hierarchical data, and traverse the tree in various orders. Aggregate, cumulate, print, plot, convert to and from data.frame and more. Useful for decision trees, machine learning, finance, conversion from and to JSON, and many other applications.

Maintained by Christoph Glur. Last updated 5 months ago.

7.2 match 209 stars 12.84 score 1.1k scripts 88 dependents

tidyverse

dtplyr:Data Table Back-End for 'dplyr'

Provides a data.table backend for 'dplyr'. The goal of 'dtplyr' is to allow you to write 'dplyr' code that is automatically translated to the equivalent, but usually much faster, data.table code.

Maintained by Hadley Wickham. Last updated 2 months ago.

datatable dplyr

5.6 match 671 stars 16.27 score 2.5k scripts 147 dependents

modesto-escobar

wikiTools:Tools for Wikidata and Wikipedia

A set of wrappers intended to check, read and download information from the Wikimedia sources. It is specifically created to work with names of celebrities, in which case their information and statistics can be downloaded. Additionally, it also builds links and snippets to use in combination with the function gallery() in netCoin package.

Maintained by Modesto Escobar. Last updated 8 months ago.

18.0 match 2 stars 5.08 score 2 scripts

trevorld

datetimeoffset:Datetimes with Optional UTC Offsets and/or Heterogeneous Time Zones

Supports import/export for a number of datetime string standards and R datetime classes often including lossless re-export of any original reduced precision including 'ISO 8601' <https://en.wikipedia.org/wiki/ISO_8601> and 'pdfmark' <https://opensource.adobe.com/dc-acrobat-sdk-docs/library/pdfmark/> datetime strings. Supports local/global datetimes with optional UTC offsets and/or (possibly heterogeneous) time zones with up to nanosecond precision.

Maintained by Trevor L. Davis. Last updated 2 months ago.

17.3 match 6 stars 5.26 score 1 scripts 2 dependents

ikosmidis

cranly:Package Directives and Collaboration Networks in CRAN

Core visualizations and summaries for the CRAN package database. The package provides comprehensive methods for cleaning up and organizing the information in the CRAN package database, for building package directives networks (depends, imports, suggests, enhances, linking to) and collaboration networks, producing package dependence trees, and for computing useful summaries and producing interactive visualizations from the resulting networks and summaries. The resulting networks can be coerced to 'igraph' <https://CRAN.R-project.org/package=igraph> objects for further analyses and modelling.

Maintained by Ioannis Kosmidis. Last updated 3 years ago.

network-analysis network-visualization

13.3 match 49 stars 6.85 score 32 scripts 1 dependents

ewenharrison

finalfit:Quickly Create Elegant Regression Results Tables and Plots when Modelling

Generate regression results tables and plots in final format for publication. Explore models and export directly to PDF and 'Word' using 'RMarkdown'.

Maintained by Ewen Harrison. Last updated 7 months ago.

7.9 match 270 stars 11.43 score 1.0k scripts

winvector

rquery:Relational Query Generator for Data Manipulation at Scale

A piped query generator based on Edgar F. Codd's relational algebra, and on production experience using 'SQL' and 'dplyr' at big data scale. The design represents an attempt to make 'SQL' more teachable by denoting composition by a sequential pipeline notation instead of nested queries or functions. The implementation delivers reliable high performance data processing on large data systems such as 'Spark', databases, and 'data.table'. Package features include: data processing trees or pipelines as observable objects (able to report both columns produced and columns used), optimized 'SQL' generation as an explicit user visible table modeling step, plus explicit query reasoning and checking.

Maintained by John Mount. Last updated 2 years ago.

9.4 match 110 stars 9.53 score 126 scripts 3 dependents

cloudyr

googleComputeEngineR:R Interface with Google Compute Engine

Interact with the 'Google Compute Engine' API in R. Lets you create, start and stop instances in the 'Google Cloud'. Support for preconfigured instances, with templates for common R needs.

Maintained by Mark Edmondson. Last updated 1 days ago.

api cloud-computing cloudyr google-cloud googleauthr launching-virtual-machines

9.2 match 152 stars 9.73 score 235 scripts

fangzhou-xie

rethnicity:Predicting Ethnic Group from Names

Implementation of the race/ethnicity prediction method, described in "rethnicity: An R package for predicting ethnicity from names" by Fangzhou Xie (2022) <doi:10.1016/j.softx.2021.100965> and "Rethnicity: Predicting Ethnicity from Names" by Fangzhou Xie (2021) <doi:10.48550/arXiv.2109.09228>.

Maintained by Fangzhou Xie. Last updated 4 days ago.

ethnicity-classifier ethnicity-prediction lstm cpp

15.8 match 9 stars 5.66 score 17 scripts

bioc

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.

motifannotation sequencematching software

17.4 match 5.08 score 60 scripts

bioc

ontoProc:processing of ontologies of anatomy, cell lines, and so on

Support harvesting of diverse bioinformatic ontologies, making particular use of the ontologyIndex package on CRAN. We provide snapshots of key ontologies for terms about cells, cell lines, chemical compounds, and anatomy, to help analyze genome-scale experiments, particularly cell x compound screens. Another purpose is to strengthen development of compelling use cases for richer interfaces to emerging ontologies.

Maintained by Vincent Carey. Last updated 3 days ago.

infrastructure go bioinformatics genomics ontology

13.8 match 3 stars 6.37 score 75 scripts 2 dependents