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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
http://cran.r-project.org/src/contrib/Archive/postgwas/
A comprehensive software toolkit for post-processing, visualization and advanced analysis of GWAS results.
Proper citation: Postgwas (RRID:SCR_000156) Copy
http://www.bioconductor.org/packages/release/bioc/html/MIMOSA.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for modeling count data using Dirichlet-multinomial and beta-binomial mixtures with applications to single-cell assays.
Proper citation: MIMOSA (RRID:SCR_000184) Copy
http://www.bioconductor.org/packages/release/bioc/html/iASeq.html
Software that uses a Bayesian hierarchical mixture model to learn correlation patterns of allele-specificity among multiple proteins.
Proper citation: iASeq (RRID:SCR_000420) Copy
http://www.bioconductor.org/packages/release/bioc/html/rTANDEM.html
An R/Bioconductor package that interfaces the X!Tandem protein identification algorithm.
Proper citation: rTANDEM (RRID:SCR_000409) Copy
https://github.com/yongchao/flowPeaks
Software for fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.
Proper citation: flowPeaks (RRID:SCR_000407) Copy
Open source and enterprise ready professional software for R statistical computing environment. Integrated development environment for R. Includes console, syntax highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. Available in open source and commercial editions and runs on desktop Windows, Mac, and Linux or in browser connected to RStudio Server or RStudio Server Pro (Debian/Ubuntu, RedHat/CentOS, and SUSE Linux).
Proper citation: RStudio (RRID:SCR_000432) Copy
http://www.bioconductor.org/packages/release/bioc/html/QUALIFIER.html
Software that provides quality control and quality assessment tools for gated flow cytometry data.
Proper citation: QUALIFIER (RRID:SCR_000389) Copy
Software tool for association study of high-dimensional microRNA expression data with repeated measures. The penalized regression model incorporates a grid search method for analyzing associations of high-dimensional microRNA expression data with repeated measures.
Proper citation: PGS (RRID:SCR_000475) Copy
Software package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Mfuzz (RRID:SCR_000523) Copy
https://cran.r-project.org/src/contrib/Archive/sybil/
A Systems Biology Library for R, implementing algorithms for constraint based analyses of metabolic networks (e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis). This is an implementation of COBRA toolbox in R language.
Proper citation: sybil - Efficient Constrained Based Modelling in R (RRID:SCR_000457) Copy
http://bioconductor.org/packages/release/bioc/html/Rdisop.html
Software for identification of metabolites using high precision mass spectrometry. MS Peaks are used to derive a ranked list of sum formulae, alternatively for a given sum formula the theoretical isotope distribution can be calculated to search in MS peak lists.
Proper citation: Rdisop (RRID:SCR_000453) Copy
https://github.com/PacificBiosciences/stsPlots
Software to plot primary analysis quality control metrics to assess potential SMRTcell loading problems.
Proper citation: stsPlots (RRID:SCR_000449) Copy
http://bioconductor.org/packages/release/bioc/html/flipflop.html
Software that discovers which isoforms of a gene are expressed in a given sample together with their abundances, based on RNA-Seq read data.
Proper citation: FlipFlop (RRID:SCR_000625) Copy
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
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
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
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
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
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
Software R package of igraph network analysis library.
Proper citation: igraph for R (RRID:SCR_021238) Copy
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