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http://wpicr.wpic.pitt.edu/WPICCompGen/blocks.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software application aiming at identifying haplotype blocks. The likelihood of the data is calculated minus the model complexity. The resulting blocks have very low diversity and the linkage disequilibrium with SNP's outside the blocks is low. (entry from Genetic Analysis Software)

Proper citation: ENTROPY BLOCKER (RRID:SCR_000123) Copy   

•   Source: SciCrunch Registry

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

Software application that is a stepwise approach to identifying recombination breakpoints in a sequence alignment (entry from Genetic Analysis Software)

Proper citation: R/STEPWISE (RRID:SCR_007420) Copy   

•   Source: SciCrunch Registry

http://wpicr.wpic.pitt.edu/WPICCompGen/

Software application (entry from Genetic Analysis Software)

Proper citation: R/SPECTRAL-GEM (RRID:SCR_007414) Copy   

•   Source: SciCrunch Registry

http://pbil.univ-lyon1.fr/software/mareymap/

Software application that is a meiotic recombination rate estimation program. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MAREYMAP (RRID:SCR_009066) Copy   

•   Source: SciCrunch Registry

http://research.nhgri.nih.gov/software/TRAP/

Software tool for determining a regression model of quantitative or binary trait variation when the number of possible genetic predictors is very large, considering only a moderate number of predictors at one time, using unrelated or family data. (entry from Genetic Analysis Software)

Proper citation: TRAP (RRID:SCR_009002) Copy   

•   Source: SciCrunch Registry

https://github.com/gaow/genetic-analysis-software/blob/master/pages/SIMULAPLOT.md

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. A tool designed to help visualize the joint effect of genes and continuous environmental covariates on complex human disease simulation models.

Proper citation: SIMULAPLOT (RRID:SCR_009079) Copy   

•   Source: SciCrunch Registry

http://www.stat.auckland.ac.nz/~browning/ccrel/ccrel.htm

Software program for case-control genetic analysis that takes relatedness between individuals into account. It will perform single-marker and haplotypic tests, however it will only work with SNP or other biallelic markers. (entry from Genetic Analysis Software)

Proper citation: CCREL (RRID:SCR_009142) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/resources/software/peer/

Software collection of Bayesian approaches to infer hidden determinants and their effects from gene expression profiles using factor analysis methods. Applications of PEER have * detected batch effects and experimental confounders * increased the number of expression QTL findings by threefold * allowed inference of intermediate cellular traits, such as transcription factor or pathway activations This project offers an efficient and versatile C++ implementation of the underlying algorithms with user-friendly interfaces to R and python.

Proper citation: PEER (RRID:SCR_009326) Copy   

•   Source: SciCrunch Registry

http://www.pedvizapi.org/

A Java Api for the visual analysis of large and complex pedigrees that provides all the necessary functionality for the interactive exploration of extended genealogies. Available packages are mostly focused on a static representation or cannot be added to an existing application; the goal of this open-source library is to provide an application program interface that enables the efficient construction of visual analytic applications for the analysis of family based data. (entry from Genetic Analysis Software)

Proper citation: PEDVIZAPI (RRID:SCR_009325) Copy   

•   Source: SciCrunch Registry

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

An R package that creates publishable-quality plots of p-values using single SNP and/or haplotype data. Main features of the package include options to display a linkage disequilibrium (LD) plot and the ability to plot multiple sets of results simultaneously. Plots can be created using global and/or individual haplotype p-values along with single SNP p-values. Images are created as either Portable Document Format (PDF) or Encapsulated (EPS) files. (entry from Genetic Analysis Software)

Proper citation: R/SNP.PLOTTER (RRID:SCR_009376) Copy   

•   Source: SciCrunch Registry

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

An R package that uses an individual-based approach to simulate distributions of genotypes that result from arbitrary within and among population demographies (including extinction/recolonization). These distributions can be used to test new or existing population-genetics summary statistics or develop null distributions under various demographies. (entry from Genetic Analysis Software)

Proper citation: R/METASIM (RRID:SCR_009370) Copy   

•   Source: SciCrunch Registry

http://research.nhgri.nih.gov/ROMPrev/

Software tool for testing for association between polymorphisms and quantitative traits, as well as estimating trait heritability and locus-specific heritability using family data. (entry from Genetic Analysis Software)

Proper citation: ROMPREV (RRID:SCR_009361) Copy   

•   Source: SciCrunch Registry

https://github.com/mikelove/tximport

Software R package for importing pseudoaligned reads into R for use with downstream differential expression analysis. Used for import and summarize transcript level estimates for transcript and gene level analysis.

Proper citation: tximport (RRID:SCR_016752) Copy   

•   Source: SciCrunch Registry

https://github.com/theislab/scanpy

Software Python tool for large scale single cell gene expression data analysis. Integrates analysis possibilities of established R-based frameworks, provides pre processing, visualization, graph-drawing and diffusion maps, clustering, identification of marker genes for clusters via differential expression tests and pseudo temporal ordering via diffusion pseudo time.

Proper citation: scanpy (RRID:SCR_018139) Copy   

•   Source: SciCrunch Registry

https://github.com/JinmiaoChenLab/Rphenograph

Software R tool as simple R implementation of PhenoGraph algorithm, which is clustering method designed for high dimensional single cell data analysis.

Proper citation: Rphenograph (RRID:SCR_022603) Copy   

•   Source: SciCrunch Registry

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

Workflow software to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.

Proper citation: RMassBank (RRID:SCR_002797) Copy   

•   Source: SciCrunch Registry

https://zeppelin.apache.org/

Web based notebook that enables data driven, interactive data analytics and collaborative documents with SQL, Scala, Python, R and more. Multi purposed web based notebook which brings data ingestion, data exploration, visualization, sharing and collaboration.

Proper citation: Apache Zeppelin (RRID:SCR_023637) Copy   

•   Source: SciCrunch Registry

http://galton.uchicago.edu/~junzhang/LAPSTRUCT.html

Software application to describe population structure using biomarker data ( typically SNPs, CNVs etc.) available in a population sample. The main features different from PCA are: (1) geometrically motivated and graphic model based; (2)robustness of outliers. (entry from Genetic Analysis Software)

Proper citation: LAPSTRUCT (RRID:SCR_007550) Copy   

•   Source: SciCrunch Registry

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

Software package implements Bayesian multilevel models in R using probabilistic programming language Stan.

Proper citation: brms (RRID:SCR_023862) Copy   

•   Source: SciCrunch Registry

http://wpicr.wpic.pitt.edu/WPICCompGen/fdr/

Software application (entry from Genetic Analysis Software)

Proper citation: WEIGHTED FDR (RRID:SCR_013442) Copy   

•   Source: SciCrunch Registry