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Issue
http://www.nitrc.org/projects/plink
Open source whole genome association analysis toolset, designed to perform range of basic, large scale analyses in computationally efficient manner. Used for analysis of genotype/phenotype data. Through integration with gPLINK and Haploview, there is some support for subsequent visualization, annotation and storage of results. PLINK 1.9 is improved and second generation of the software.
Proper citation: PLINK (RRID:SCR_001757) Copy
Issue
https://biit.cs.ut.ee/clustvis/
Web user interface for visualizing clustering of multivariate data. Web server allows users to upload their own data and create Principal Component Analysis plots and heatmaps.
Proper citation: ClustVis (RRID:SCR_017133) Copy
Issue
https://biology-assets.anu.edu.au/GenAlEx/Welcome.html
Software tool as cross platform package for population genetic analyses that runs within Microsoft Excel. Offers analysis of diploid codominant, haploid and binary genetic loci and DNA sequences.Originally developed as teaching tool to facilitate teaching population genetic analysis at graduate level.
Proper citation: GenAlEx (RRID:SCR_021102) Copy
Issue
https://github.com/gabraham/flashpca
Software tool as fast principal component analysis of large scale genome wide data. FlashPCA performs fast principal component analysis (PCA) of single nucleotide polymorphism (SNP) data. FlashPCA2 used for principal component analysis of biobank scale genotype datasets.
Proper citation: FlashPCA (RRID:SCR_021680) Copy
Issue
https://www.nature.com/articles/nprot.2014.042
Software tool as scripts for calculating NMR chemical shifts. Warning - this group of Python scripts used to process NMR data, described in Willoughby et al, 2014, has been found to contain bug. Please see PMID:31591889.
Proper citation: Willoughby–Hoye Python Scripts A-D (RRID:SCR_017562) Copy
Issue
https://cran.r-project.org/web/packages/adegenet/index.html
Software package dedicated to the handling of molecular marker data for multivariate analysis. This package is related to ADE4, a R package for multivariate analysis, graphics, phylogeny and spatial analysis. (entry from Genetic Analysis Software)
Proper citation: ADEGENET (RRID:SCR_000825) Copy
Issue
https://reich.hms.harvard.edu/software
EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker''s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes. Source code, documentation and executables for using EIGENSOFT 3.0 on a Linux platform can be downloaded. New features of EIGENSOFT 3.0 include supporting either 32-bit or 64-bit Linux machines, a utility to merge different data sets, a utility to identify related samples (accounting for population structure), and supporting multiple file formats for EIGENSTRAT stratification correction.
Proper citation: Eigensoft (RRID:SCR_004965) Copy
Issue
https://cran.r-project.org/package=pcadapt
Software R package for fast Principal Component Analysis for outlier detection.Used to detect genetic markers involved in biological adaptation. Performs genome scans for selection based on principal component analysis.
Proper citation: pcadapt (RRID:SCR_022019) Copy
Issue
Software package for analysis of brain imaging data sequences. Sequences can be a series of images from different cohorts, or time-series from same subject. Current release is designed for analysis of fMRI, PET, SPECT, EEG and MEG.
Proper citation: SPM (RRID:SCR_007037) Copy
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