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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   

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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

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

R package that takes a list of p-values resulting from the simultaneous testing of hypotheses and estimates their q-values. It is designed to measure the proportion of false positives when a test is significant. The software is capable of generating plots for visualization. It can be applied to problems in genomics, brain imaging, astrophysics, and data mining.

Proper citation: Qvalue (RRID:SCR_001073) Copy   

•   Source: SciCrunch Registry

http://www2.hu-berlin.de/wikizbnutztier/software/CandiSNPer/

A webtool which helps in characterizing Single Nucleotide Polymorphisms (SNPs) that are located in the vicinity of an SNP of interest (start SNP). Along with the computation of the maximal Linkage Disequilibrium (LD) region around the start SNP. CandiSNPer provides additional information with respect to the molecular consequences of the SNPs and the genes located in the LD region.

Proper citation: CandiSNPer (RRID:SCR_005173) Copy   

•   Source: SciCrunch Registry

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

Softare R package as implementation of the t-SNE algorithm.

Proper citation: tsne (RRID:SCR_024305) Copy   

•   Source: SciCrunch Registry

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://atgu.mgh.harvard.edu/plinkseq/

An open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing projects, particularly whole-exome and whole-genome studies. However, the library could in principle be applied to other types of genetic studies, including whole-genome association studies of common SNPs. (entry from Genetic Analysis Software)

Proper citation: PLINK/SEQ (RRID:SCR_013193) 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

https://igraph.org/r/

Software R package of igraph network analysis library.

Proper citation: igraph for R (RRID:SCR_021238) Copy   

•   Source: SciCrunch Registry

http://zzlab.net/blink/index.html

Software for next level of genome wide association studies with both individuals and markers in millions. The method releases the requirement that causative genes are evenly distributed on genome and consequently boosts statistical power.

Proper citation: BLINK (RRID:SCR_016288) Copy   

•   Source: SciCrunch Registry

https://rpy2.github.io/

Software interface to use R from Python.

Proper citation: rpy2 (RRID:SCR_024701) Copy   

•   Source: SciCrunch Registry

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

Software R package for model selection and multimodel inference. Used for automated model selection and model-averaging. Provides wrapper for glm and other functions, automatically generating all possible models with specified response and explanatory variables.

Proper citation: glmulti (RRID:SCR_025423) 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

https://bioconductor.org/packages/release/bioc/html/SomaticSignatures.html

Software R package for identifying mutational signatures of single nucleotide variants (SNVs) from high-throughput experiments.

Proper citation: SomaticSignatures (RRID:SCR_025620) Copy   

•   Source: SciCrunch Registry