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

An R-package which uses Object Oriented Data Analysis (OODA) methods to analyze taxonomic trees directly, providing tools to model, compare, and visualize populations of taxonomic tree objects.

Proper citation: HMPTrees (RRID:SCR_014613) Copy   

•   Source: SciCrunch Registry

https://github.com/dgrapov/CTSgetR

R interface to Chemical Translation Service which provides translation between chemical and biological database identifiers.

Proper citation: CTSgetR (RRID:SCR_014672) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/krux/

An algorithm implemented in Matlab, Python and R that uses matrix multiplications to simultaneously calculate the Kruskal-Wallis test statistic for several millions of marker-trait combinations at once.

Proper citation: kruX (RRID:SCR_012076) Copy   

•   Source: SciCrunch Registry

http://xmsanalyzer.sourceforge.net

A software package of utilities for data extraction, quality control assessment, detection of overlapping and unique metabolites in multiple datasets, and batch annotation of metabolites. xMSanalyzer comprises of utilities that can be classified into five main modules: 1) merging apLCMS or XCMS sample processing results from multiple sets of parameter settings, 2) evaluation of sample quality, feature consistency, and batch-effect, 3) feature matching, and 4) characterization of m/z using KEGG REST; 5) Batch-effect correction using ComBat.

Proper citation: xMSanalyzer (RRID:SCR_012144) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/PICS.html

R package with tools that use probabilistic inference of ChIP-Seq. It follows an empirical Bayes mixture model approach.

Proper citation: PICS (RRID:SCR_001093) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/rfmri/

The package fmri provides fMRI analysis with R using structural adaptive smoothing methods. They allow smoothing especially at low SNR avoiding the apparent blurring of non-adapative smoothing and thus without reducing the effective spatial resolution.

Proper citation: R-package for adaptive fMRI analysis (RRID:SCR_002530) Copy   

•   Source: SciCrunch Registry

https://www.synapse.org/

A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data.

Proper citation: Synapse (RRID:SCR_006307) Copy   

•   Source: SciCrunch Registry

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

Software R package for basic statistical tests including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and correlation analyses. Output of each test is automatically transformed into data frame to facilitate visualization. Additional functions are available for reshaping, reordering, manipulating and visualizing correlation matrix. Functions are also included to facilitate analysis of factorial experiments. Can compute several effect size metrics.Package contains helper functions for identifying univariate and multivariate outliers, assessing normality and homogeneity of variances.

Proper citation: rstatix (RRID:SCR_021240) Copy   

•   Source: SciCrunch Registry

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

Software application that plots measures of pairwise linkage disequilibria for SNPs (entry from Genetic Analysis Software)

Proper citation: LDHEATMAP (RRID:SCR_006312) Copy   

•   Source: SciCrunch Registry

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

Software application that is a simple clustering method that can be used to rapidly identify a set of tag SNP's based upon genotype data (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: HCLUST (RRID:SCR_009154) Copy   

•   Source: SciCrunch Registry

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

A software package that provides functions to read raw RT-qPCR data of different platforms.

Proper citation: ReadqPCR (RRID:SCR_000030) Copy   

•   Source: SciCrunch Registry

http://decipher.cee.wisc.edu/index.html

A software toolset that can be used for deciphering and managing DNA sequences efficiently using the R statistical programming language., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Database Enabled Code for Ideal Probe Hybridization Employing R (RRID:SCR_000581) Copy   

•   Source: SciCrunch Registry

http://www.rstudio.com/shiny/

Open source R package that provides web framework for building web applications using R. Used to create interactive web apps in native R, without needing to use HTML, CSS, or JavaScript.

Proper citation: Shiny (RRID:SCR_001626) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/carol

Software application that is a combined functional annotation score of non-synonymous coding variants. A major challenge in interpreting whole-exome data is predicting which of the discovered variants are deleterious or neutral. To address this question in silico, they have developed a score called Combined Annotation scoRing toOL (CAROL), which combines information from two bioinformatics tools: PolyPhen-2 and SIFT, in order to improve the prediction of the effect of non-synonymous coding variants. The combination of annotation tools can help improve automated prediction of whole-genome/exome non-synonymous variant functional consequences. (entry from Genetic Analysis Software) The software should run on any UNIX or GNU/Linux system.

Proper citation: CAROL (RRID:SCR_001800) Copy   

•   Source: SciCrunch Registry

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

Network of ftp and web servers around world that store identical, up to date, versions of code and documentation for R. Package archive network for R programming language.

Proper citation: CRAN (RRID:SCR_003005) Copy   

•   Source: SciCrunch Registry

https://github.com/acnash/CPRD_Additional_Clinical/blob/master/CPRDLooksups.R

Software R tool used to identify and retrieve CPRD clinical additional record information such as, smoking, weight/BMI, and medical tests.

Proper citation: CPRDLooksups.R (RRID:SCR_018959) Copy   

•   Source: SciCrunch Registry

http://www.stats.ox.ac.uk/%7Emarchini/software.html

An R package that specifically focuses on statistical and population genetics methods. The motivation behind the package is to produce an easy to use interface to many of the commonly used methods and models used in statistical and population genetics and an alternative interface for some of the methodology produced by our group. (entry from Genetic Analysis Software)

Proper citation: POPGEN (RRID:SCR_007315) Copy   

•   Source: SciCrunch Registry

http://www.sph.umich.edu/csg/abecasis/Exact/index.html

Software application for a fast exact Hardy-Weinberg Equilibrium test for SNPs (entry from Genetic Analysis Software)

Proper citation: SNP-HWE (RRID:SCR_008555) Copy   

•   Source: SciCrunch Registry

http://www.modelmakertools.com/modelmaker/index.html

Multi-threaded, parallel and CUDA based application that provides an interface to the R statistical language, MATLAB, Accord and Aforge APIs, along with Neural Maestro to accomplish fMRI, EEG, speech signals, commodity price analysis, general machine learning, classification and time series analysis and forecasting. Because it unifies research development work in MATLAB, R and C++, it provides a mathematical canvas the permits researches to experiment with both pure and hybrid models that use the best of all software development languages.

Proper citation: ModelMaker (RRID:SCR_009024) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/meta/index.html

Software application for fixed and random effects meta-analysis. Functions for tests of bias, forest and funnel plot. (entry from Genetic Analysis Software)

Proper citation: R/META (RRID:SCR_009175) Copy   

•   Source: SciCrunch Registry