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http://cran.r-project.org/web/packages/kdetrees/

R package using a non-parametric method for estimating distributions of phylogenetic trees, with the goal of identifying trees that are significantly different from the rest of the trees in the sample.

Proper citation: Kdetrees (RRID:SCR_004522) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/ExomeDepth/

Software that calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.

Proper citation: ExomeDepth (RRID:SCR_002663) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/pairheatmap/

A software tool to compare two heatmaps and discover patterns within and across groups. In the context of biology, group can be defined based on gene ontology.

Proper citation: pairheatmap (RRID:SCR_003109) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/isa2/

A biclustering algorithm that finds modules in an input matrix. A module or bicluster is a block of the reordered input matrix.

Proper citation: Iterative Signature Algorithm (RRID:SCR_002327) 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

http://cran.r-project.org/web/packages/MultiPhen/

Software package that performs genetic association tests between SNPs (one-at-a-time) and multiple phenotypes (separately or in joint model).

Proper citation: MultiPhen (RRID:SCR_003498) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/src/contrib/Archive/PurBayes/

An MCMC-based algorithm that uses next-generation sequencing data to estimate tumor purity and clonality for paired tumor-normal data.

Proper citation: PurBayes (RRID:SCR_002068) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/VennDiagram/

Software providing a set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure.

Proper citation: VennDiagram (RRID:SCR_002414) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/circlize/

Software package that implements and enhances circular visualization in R. Due to natural born feature of R to draw statistical graphics, this package can provide more general and flexible way to visualize huge information in circular style.

Proper citation: circlize (RRID:SCR_002141) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/lme4/index.html

Software R package. Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue."

Proper citation: lme4 (RRID:SCR_015654) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/PSCBS/

Software R package for segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.

Proper citation: PSCBS (RRID:SCR_000417) Copy   

•   Source: SciCrunch Registry

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

Software R package for analysis of phylogenetics and evolution. Environment for modern phylogenetics and evolutionary analyses in R.

Proper citation: ape (RRID:SCR_017343) Copy   

•   Source: SciCrunch Registry

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

Software R package for phylogenetic reconstruction and analysis. Used for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation. Allows to compare trees, models selection and offers visualizations for trees and split networks.

Proper citation: Phangorn (RRID:SCR_017302) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/ggtree/

Software R package for visualization and annotation of phylogenetic trees with their covariates and other tree like structures with their annotation data. Can import evolutionary data from different tree file formats and analysis programs as well as other associated data from experiments so that various sources and types of data can be displayed on tree for comparison and further analyses.

Proper citation: ggtree (RRID:SCR_018560) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/timecourse.html

Software functions for data analysis and graphical displays for developmental microarray time course data.

Proper citation: timecourse (RRID:SCR_000077) Copy   

•   Source: SciCrunch Registry

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

Software environment and programming language for statistical computing and graphics. R is integrated suite of software facilities for data manipulation, calculation and graphical display. Can be extended via packages. Some packages are supplied with the R distribution and more are available through CRAN family.It compiles and runs on wide variety of UNIX platforms, Windows and MacOS.

Proper citation: R Project for Statistical Computing (RRID:SCR_001905) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/package=psych

Software R package for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis.Procedures for Psychological, Psychometric, and Personality Research. Used for personality, psychometric theory and experimental psychology.

Proper citation: psych (RRID:SCR_021744) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/GALLO/vignettes/GALLO.html

Software R package developed for accurate annotation of genes and quantitative trait loci located in regions identified in common genomic analyses performed in livestock, such as Genome Wide Association Studies and transcriptomics using RNA-Sequencing. Allows graphical visualization of gene and QTL annotation results, data comparison among different grouping factors like methods, breeds, tissues, statistical models, studies and QTL enrichment in different livestock species including cattle, pigs, sheep, and chickens.

Proper citation: Genomic Annotation in Livestock for positional candidate LOci (RRID:SCR_019212) Copy   

•   Source: SciCrunch Registry

https://github.com/hms-dbmi/EHRtemporalVariability

Software R package for delineating temporal dataset shifts in electronic health records. Functions to delineate temporal dataset shifts in electronic health records through projection and visualization of dissimilarities among data temporal batches.Enables exploration and identification of dataset shifts, contributing to broadly examine and repurpose large, longitudinal datasets. Used to help ensure reliable data reuse to biomedical data users.

Proper citation: EHRtemporalVariability (RRID:SCR_018663) Copy   

•   Source: SciCrunch Registry