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https://CRAN.R-project.org/package=tidyverse
Software tool as collection of R packages designed for data science which share underlying design philosophy, grammar, and data structures. Packages work in harmony because they share common data representations and API design. Used in everyday data analyses.
Proper citation: tidyverse (RRID:SCR_019186) Copy
https://CRAN.R-project.org/package=simr
Software R package for power analysis of generalized linear mixed models by simulation. Used to calculate power for generalised linear mixed models.
Proper citation: SIMR (RRID:SCR_019287) Copy
https://CRAN.R-project.org/package=gbs2ploidy
Software R package as functions for inference of ploidy from Genotyping By Sequencing data, including function to infer allelic ratios and allelic proportions in Bayesian framework.
Proper citation: gbs2ploidy (RRID:SCR_019290) Copy
https://CRAN.R-project.org/package=spdep
Software R package as collection of functions to create spatial weights matrix objects from polygon contiguities, from point patterns by distance and tessellations, for summarizing these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree.
Proper citation: spdep (RRID:SCR_019294) Copy
https://cran.r-project.org/web/packages/igraph/
Software package for graphs and network analysis. Provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.Can be programmed in R, Python, Mathematica, C/C Plus Plus.
Proper citation: igraph (RRID:SCR_019225) Copy
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
https://bioconductor.org/packages/variancePartition/
Software R package to quantify and interpret divers of variation in multilevel gene expression experiments.Provides statistical and visualization framework for studying drivers of variation in RNA-seq datasets in many types of high throughput genomic assays including RNA-seq gene-, exon- and isoform-level quantification, splicing efficiency, protein quantification, metabolite quantification, metagenomic assays, methylation arrays and epigenomic sequencing assays.
Proper citation: variancePartition (RRID:SCR_019204) Copy
http://cran.r-project.org/web/packages/metaMA/
Software R package for meta-analysis for microarrays. It combines either p-values or modified effect sizes from different studies to find differentially expressed genes.
Proper citation: metaMA (RRID:SCR_000408) Copy
https://cran.r-project.org/web/packages/MIIVsem/index.html
Software R package for estimating structural equation models using instrumental variables.
Proper citation: MIIVsem (RRID:SCR_017444) Copy
https://cran.r-project.org/web/packages/viridis/vignettes/intro-to-viridis.html
Software package which brings to R color scales. Created for the Python matplotlib library.
Proper citation: viridis (RRID:SCR_016696) Copy
http://CRAN.R-project.org/package=RVAideMemoire
Software package that contains miscellaneous functions useful in biostatistics, such as univariate and multivariate testing procedures with a special emphasis on permutation tests. Many functions shorten existing procedures and implement plotting functions that can be used with a variety of methods and packages.
Proper citation: R package: RVAideMemoire (RRID:SCR_015657) Copy
https://github.com/benmarwick/cvequality
Software R package contains functions to test for significant differences in coefficients of variation among multiple groups of observations.
Proper citation: cvequality (RRID:SCR_019124) Copy
https://cran.r-project.org/web/packages/gtsummary/index.html
Software R package creating customizable presentation ready tables, summarizing data sets, regression models, and more. Used for publication ready data summary and analytic result tables.
Proper citation: gtsummary (RRID:SCR_021319) Copy
https://CRAN.R-project.org/package=mHG
Software R package to run minimum hypergeometric test.
Proper citation: Minimum-Hypergeometric Test (RRID:SCR_018776) Copy
https://CRAN.R-project.org/package=survival
Software R package contains core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.
Proper citation: survival (RRID:SCR_021137) Copy
https://CRAN.R-project.org/package=caret
Software R package provides misc functions for training and plotting classification and regression models.Contains tools for data splitting, pre-processing, feature selection, model tuning using resampling, and variable importance estimation, as well as other functionality.
Proper citation: caret (RRID:SCR_021138) Copy
https://CRAN.R-project.org/package=openxlsx
Software R package to simplify creation of .xlsx files by providing high level interface to writing, styling and editing worksheets.
Proper citation: openxlsx (RRID:SCR_019185) Copy
https://CRAN.R-project.org/package=meta
Software general R package providing standard methods for meta analysis.
Proper citation: meta (RRID:SCR_019055) Copy
https://cran.r-project.org/package=CCP
Software R package for significance tests for canonical correlation analysis, including asymptotic tests and Monte Carlo method.
Proper citation: CCP (RRID:SCR_021745) Copy
https://bioconductor.org/packages/FilterFFPE/
Software R package to find and filter artificial chimeric reads specifically generated in next generation sequencing process of formalin fixed paraffin embedded tissues. These artificial chimeric reads can lead to large number of false positive structural variant calls. Artifact chimeric read filter to improve SV detection in FFPE samples.
Proper citation: FilterFFPE (RRID:SCR_021086) Copy
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