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

Software application that employs allele matching to analyse the effects of rare variants within a specific locus. There is increasing evidence that rare variants play a role in some complex traits, but their analysis is not straightforward. Locus-based tests become necessary due to low power in rare variant single-point association analyses. In addition, variant quality scores are available for sequencing data, but are rarely taken into account. To enable this analysis, AMELIA has been developed as an allele-matching approach that is robust to the presence of both directions of effect for variants within the locus analysed. (entry from Genetic Analysis Software)

Proper citation: AMELIA (RRID:SCR_009119) Copy   

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http://gump.qimr.edu.au/GAIA/gaia.html

Web-based application for testing for locus-locus interaction using genetic association. It is based upon the case-control study design and is designed so that non-specialists may routinely apply tests for interaction. GAIA allows simple testing of both additive and additive plus dominance interaction models and includes permutation testing to appropriately correct for multiple testing. The application is useful for both candidate gene based studies and genome-wide association studies. For large scale studies GAIA includes a screening approach which prioritizes loci for further interaction analysis. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GAIA (RRID:SCR_009182) Copy   

•   Source: SciCrunch Registry

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

Software application that explores the effects of rare variants within complex traits through locus-based analysis. There is increasing evidence that rare variants play a role in some complex traits, but their analysis is not straightforward. Locus-based tests become necessary due to low power in rare variant single-point association analyses. In addition, variant quality scores are available for sequencing data, but are rarely taken into account. To enable this analysis, ARIEL has been developed as a locus-wide regression-based collapsing approach that incorporates variant quality scores. (entry from Genetic Analysis Software)

Proper citation: ARIEL (RRID:SCR_009126) Copy   

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http://www.stats.ox.ac.uk/~marchini/software.html

A R package for assessing the power of genome-wide association studies using commercially available genotyping chips. The package encapsulates extensive simulation results generated by our program HAPGEN. (entry from Genetic Analysis Software)

Proper citation: GWAPOWER (RRID:SCR_009216) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/fastcluster/1.2.3/

Software Python library for hierarchical clustering. Fast Hierarchical, Agglomerative Clustering Routines for R and Python.

Proper citation: fastcluster (RRID:SCR_023597) Copy   

•   Source: SciCrunch Registry

http://connectir.projects.nitrc.org

An R-based package to conduct brain connectivity analyses with a focus on a novel approach to conducting Connectome-Wide Association Studies (CWAS) using functional connectivity.

Proper citation: Connectir (RRID:SCR_000863) Copy   

•   Source: SciCrunch Registry

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

Software package that provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry. It was designed for high throughput metabolomics data with many biological samples and a large numer of ion trees collected. Tests have been done with data from low-resolution mass spectrometry but could be readily extended to precursor ion based fragmentation data from high resoultion mass spectrometry.

Proper citation: iontree (RRID:SCR_002813) Copy   

•   Source: SciCrunch Registry

http://www.jstatsoft.org/v49/i08/.

Data Analysis GUI for R. The program is based on Java's Swing GUI library and includes an Excel-like spreadsheet for easy data viewing and editing.

Proper citation: R package: Deducer (RRID:SCR_015659) Copy   

•   Source: SciCrunch Registry

https://github.com/ChristofSeiler/braincog

Software package to elucidate complex interactions between subsets of neuroanatomical features and subsets of cognitive features. briancog specializes in differential correlation analysis.

Proper citation: braincog (RRID:SCR_015871) Copy   

•   Source: SciCrunch Registry

https://rdocumentation.org/packages/survminer/versions/0.4.9

Software R package provides functions for facilitating survival analysis and visualization.

Proper citation: survminer (RRID:SCR_021094) Copy   

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

Software toolkit for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control. This package facilitates pre-processing, quality control, normalization and visualization of scRNA-seq data.

Proper citation: scater (RRID:SCR_015954) Copy   

•   Source: SciCrunch Registry

https://www.jamovi.org/

Software for statistical analysis and spreadsheet editing that is built on top of the R statistical language. It encourages a “community driven” philosophy, where users can develop and publish their analyses to make them available to a wide audience.

Proper citation: jamovi (RRID:SCR_016142) Copy   

•   Source: SciCrunch Registry

http://bowtie-bio.sourceforge.net/recount/

RNA-seq gene count datasets built using the raw data from 18 different studies. The raw sequencing data (.fastq files) were processed with Myrna to obtain tables of counts for each gene. For ease of statistical analysis, they combined each count table with sample phenotype data to form an R object of class ExpressionSet. The count tables, ExpressionSets, and phenotype tables are ready to use and freely available. By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward.

Proper citation: ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets (RRID:SCR_001774) Copy   

•   Source: SciCrunch Registry

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

Software package provides R interface to NCBI EUtils API, to search databases like GenBank and PubMed, process of those searches. Provides functions that work with NCBI Eutils API to search, download data from, and otherwise interact with NCBI databases.

Proper citation: rentrez (RRID:SCR_021062) Copy   

•   Source: SciCrunch Registry

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

Software R package as functions to accompany J. Fox and S. Weisberg R companion to applied regression.

Proper citation: Companion to Applied Regression (RRID:SCR_022137) Copy   

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

Software environment for constructing linkage maps in outcrossing plant species, using full-sib families derived from two outbreed (non-inbreeding) parent plants. (entry from Genetic Analysis Software)

Proper citation: R/ONEMAP (RRID:SCR_009371) Copy   

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http://www.mrc-epid.cam.ac.uk/~jinghua.zhao/r-progs.htm

An integrated software package for genetic data analysis of both population and family data. Currently it contains functions for sample size calculations of both population-based and family-based designs, classic twin ACE/ADE/AE/CE models, probability of familial disease aggregation, kinship calculation, some statistics in linkage analysis, and association analysis involving one or more genetic markers including haplotype analysis with or without environmental covariates (entry from Genetic Analysis Software)

Proper citation: R/GAP (RRID:SCR_009364) Copy   

•   Source: SciCrunch Registry

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

Software application using a likelihood approach to inference of haplotype and nongenetic effects and their interactions in generalized linear models of disease penetrance, when haplotype phase is unknown for some subjects. Parameter estimates are obtained by use of an expectation-maximization (EM) algorithm and standard errors are calculated using Louis'' formula. (entry from Genetic Analysis Software)

Proper citation: R/HAPASSOC (RRID:SCR_009365) Copy   

•   Source: SciCrunch Registry

http://www.chg.duke.edu/research/simla30.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. Simulation program that generates data sets of families for use in linkage and association studies. SIMLA_3.2 is a major upgrade to versions 2.3 and 3.0 that provides the ability to simulate two disease loci and two environmental covariates. Gene-gene and gene-environment interactions may also be simulated which jointly determine the disease risk of all pedigree members.

Proper citation: SIMULA (RRID:SCR_009390) Copy   

•   Source: SciCrunch Registry

http://www.niehs.nih.gov/research/resources/software/epidemiology/tagster/

Software tool to select, evaluate and visualize LD tag SNPs for single or multiple populations. The input files can be a set of dumped genotype files from International HapMap Project (http://www.hapmap.org/) (Hapmap format) or Seattle SNPs (http://pga.gs.washington.edu/) (Prettybase format). The ouput is a set of LD tag SNPs for single or multiple populations. (entry from Genetic Analysis Software)

Proper citation: TAGSTER (RRID:SCR_009413) Copy   

•   Source: SciCrunch Registry