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http://cran.r-project.org/

Network of ftp and web servers around world that store identical, up to date, versions of code and documentation for R. Package archive network for R programming language.

Proper citation: CRAN (RRID:SCR_003005) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/ggplot2/index.html

Open source software package for statistical programming language R to create plots based on grammar of graphics. Used for data visualization to break up graphs into semantic components such as scales and layers.

Proper citation: ggplot2 (RRID:SCR_014601) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/metagear/index.html

Software R package for research synthesis taxonomy from applying systematic review approach to assemble and screen literature, to extract data from studies, and to summarize and analyze these data with statistics of meta analysis.

Proper citation: metagear (RRID:SCR_017085) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/seqinr/index.html

Software R package for exploratory data analysis and data visualization for biological sequence, DNA and protein, data.

Proper citation: seqinr (RRID:SCR_022678) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/taxize/index.html

Software R package for taxonomic information from around web. Interacts with suite of web 'APIs' 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.

Proper citation: taxize (RRID:SCR_022677) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=Hmisc

Software R package for data analysis, graphics, utility operations, functions for computing sample size and power, simulation, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX and html code, and recoding variables.

Proper citation: Harrell Miscellaneous (RRID:SCR_022497) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/BGLR/

Software R package implements large collection of Bayesian regression models, including parametric variable selection and shrinkage methods and semiparametric procedures.

Proper citation: Bayesian Generalized Linear Regression (RRID:SCR_022522) Copy   

•   Source: SciCrunch Registry

https://academic.oup.com/bioinformatics/article/34/7/1229/4657077

Software R/Shiny application for interactive creation of Circos plot. Used for creation of Circos plot interactively.

Proper citation: shinyCircoss (RRID:SCR_022367) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/rrBLUP/

Software R package for mixed models with single variance component besides residual error, which allows for efficient prediction with unreplicated training data. Makes ridge regression and other kernel methods accessible to plant breeders interested in genomic selection.

Proper citation: ridge regression Best Linear Unbiased Prediction (RRID:SCR_022519) Copy   

•   Source: SciCrunch Registry

https://github.com/nboley/idr

Software R package to measure reproducibility of findings identified from replicate experiments and to provide highly stable thresholds based on reproducibility.

Proper citation: IDR (RRID:SCR_017237) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/knitr/index.html

Software R package for dynamic report generation using Literate Programming techniques. Comprehensive software tool for reproducible research in R.

Proper citation: knitr (RRID:SCR_018533) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/geomorph/index.html

Software package for performing all stages of geometric morphometric shape analysis of landmark points and curves in 2-and-3-dimensions as well as 3D surfaces in the R statistical computing environment.

Proper citation: geomorph (RRID:SCR_016482) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=tidyr

Software R package for easily tidy data with spread and gather functions. Used for simplifying process of creating tidy data.

Proper citation: tidyr (RRID:SCR_017102) Copy   

•   Source: SciCrunch Registry

https://github.com/dgrun/RaceID

Algorithm for identification of rare and abundant cell types from single cell transcriptome data. Based on transcript counts obtained with unique molecular identifies. Used for discovering rare cell types and corresponding marker genes in healthy and diseased organs. Operating system Unix/Linux, Mac OS, Windows.

Proper citation: RaceID (RRID:SCR_017045) Copy   

•   Source: SciCrunch Registry

https://github.com/jkrijthe/Rtsne

Software as R wrapper for Van der Maaten's Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding. Used for high-dimentional data visualisation.

Proper citation: Rtsne (RRID:SCR_016342) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/dplyr/index.html

Software tool for working with data frame like objects, both in memory and out of memory. It is a grammar of data manipulation, providing a consistent set of verbs that help you solve the most common data manipulation challenges: mutate, select, filer, summerise, arrange.

Proper citation: dplyr (RRID:SCR_016708) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/RColorBrewer/index.html

Software tool to provide color schemes for maps and other graphics. R package to create colorful graphs with pre-made color palettes that visualize data.

Proper citation: RColorBrewer (RRID:SCR_016697) Copy   

•   Source: SciCrunch Registry

https://www.rdocumentation.org/packages/statmod/versions/1.4.30

SoftwareR package from CRAN for statistical modeling. Includes growth curve comparisons, limiting dilution analysis (aka ELDA), mixed linear models, heteroscedastic regression, inverse-Gaussian probability calculations, Gauss quadrature and a secure convergence algorithm for nonlinear models. Includes advanced generalized linear model functions that implement secure convergence, dispersion modeling and Tweedie power-law families.

Proper citation: statmod (RRID:SCR_016698) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/dendsort/index.html

Software R package from CRAN as a modular leaf ordering methods for dendrogram nodes. Used as sorting methods to improve readability and interpretability of tree structure. Used for comparison of different distance measures or linkage types, identification of tight clusters and outliers, and for coupled heatmap visualization.

Proper citation: dendsort (RRID:SCR_016693) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=NBR

Software tool as implementation of network based statistics toolbox in R. Includes mixed effects models.

Proper citation: Network-Based R-Statistics (RRID:SCR_019114) Copy   

•   Source: SciCrunch Registry