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http://wbiomed.curtin.edu.au/genepop/
Population genetic data analysis software package. Used to perform exact Hardy Weinberg Equilibrium test. Used for population differentiation and for genotypic disequilibrium among pairs of loci. Computes estimates of F-statistics, null allele frequencies, allele size-based statistics for microsatellites, etc. and performs analyses of isolation by distance from pairwise comparisons of individuals or population samples., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: GENEPOP (RRID:SCR_009194) Copy
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
https://github.com/cancerit/BRASS
Software tool for analysis of one or more related BAM files of paired end sequencing to determine potential rearrangement breakpoints. Identifies breaks and attempts to assemble rearrangements.
Proper citation: BRASS (RRID:SCR_017091) Copy
https://github.com/powellgenomicslab/ascend
Software R package for analysis of single cell RNA-seq expression, normalization and differential expression data. Provides framework to perform cell and gene filtering, quality control, normalization, dimension reduction, clustering, differential expression, and visualization functions.
Proper citation: ascend (RRID:SCR_017257) Copy
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
https://cran.r-project.org/web/packages/gbm/gbm.pdf
Software R package to implement extensions to Freund and Schapire AdaBoost algorithm and Friedman gradient boosting machine. Includes regression methods for least squares, absolute loss, t distribution loss, quantile regression, logistic, multinomial logistic, Poisson, Cox proportional hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss, and Learning to Rank measures.
Proper citation: GBM R package (RRID:SCR_017301) Copy
https://CRAN.R-project.org/package=webchem
Open source software package for R programming language that is used to acquire chemical information from online data sources. Package contains functions that allow programmer to interact with webpages and APIs to retrieve chemical information.
Proper citation: webchem (RRID:SCR_017684) Copy
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
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
https://cran.r-project.org/web/packages/readxl/index.html
Software R package to import excel files into R. Has no external dependencies for easy installment and use on all operating systems. Designed to work with tabular data.
Proper citation: readxl (RRID:SCR_018083) Copy
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
Software R package for Bayesian applied regression modeling via Stan.
Proper citation: rstanarm (RRID:SCR_024605) Copy
https://CRAN.R-project.org/package=corrplot
Software R package as visual exploratory tool on correlation matrix that supports automatic variable reordering to help detect hidden patterns among variables.Used for graphical display of correlation matrix, confidence interval. Contains some algorithms to do matrix reordering. Good at details, including choosing color, text labels, color labels, layout, etc.
Proper citation: corrplot (RRID:SCR_024683) Copy
https://www.rdocumentation.org/packages/pheatmap/versions/0.2/topics/pheatmap
Software tool as a function in R to draw clustered heatmaps for better control over graphical parameters.
Proper citation: pheatmap (RRID:SCR_016418) Copy
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
https://CRAN.R-project.org/package=pavo
Software R package for perceptual analysis, visualization and organization of spectral colour data. Software framework for parsing, analyzing and organizing colour from spectral data. Used for spectral and spatial analysis of color patterns.
Proper citation: pavo (RRID:SCR_019123) Copy
https://cran.r-project.org/web/packages/celltrackR/index.html
Software R package to analyze immune cell migration data. Supports pipeline for track analysis by providing methods for data management, quality control, extracting and visualizing migration statistics, clustering tracks, and simulating cell migration.Available measures include displacement, confinement ratio, autocorrelation, straightness, turning angle, and fractal dimension. Measures can be applied to entire tracks, steps, or subtracks with varying length.
Proper citation: celltrackR (RRID:SCR_021021) Copy
https://www.rdocumentation.org/packages/DGCA/versions/1.0.2
Software R package to perform differential gene correlation analysis. Performs differential correlation analysis on input matrices, with multiple conditions specified by design matrix.
Proper citation: Differential Gene Correlation Analysis (RRID:SCR_020964) Copy
https://bwhbioinfo.shinyapps.io/powerEQTL/
Software R package and shiny application for sample size and power calculation of bulk tissue and single-cell eQTL analysis.
Proper citation: powereQTL (RRID:SCR_021653) Copy
Software R package for exploration of single-cell and bulk T-cell/antibody immune repertoires. Framework for bioinformatics exploratory analysis of bulk and single-cell T-cell receptor and antibody repertoires.
Proper citation: immunarch (RRID:SCR_023089) Copy
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