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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   

•   Source: SciCrunch Registry

https://www.nature.com/articles/nprot.2014.131

Software tool calculates direction autocorrelation, plots and calculates other essential parameters to analyze cell migration in two dimensions: it displays cell trajectories individually and collectively, and it calculates average speed and mean square displacements (MSDs) to assess the area explored by cells over time.

Proper citation: DiPer (RRID:SCR_021720) Copy   

•   Source: SciCrunch Registry

https://www.mayo.edu/research/labs/tissue-repair-mechanobiology/software

Software tool to calculate 2D tractions exerted by adherent cell on its substrate. Used in field of mechanobiology to study contractile responses of variety of cell types.

Proper citation: TractionsForAll (RRID:SCR_021819) Copy   

•   Source: SciCrunch Registry

https://github.com/jtamames/SqueezeMeta

Software tool as fully automated pipeline for metagenomic analysis. Used for metagenomics covering all steps of analysis. Features several characteristics including co-assembly procedure or co-assembly of unlimited number of metagenomes via merging of individual assembled metagenomes, both with read mapping for estimation of abundances of genes in each metagenome. Includes binning and bin checking for retrieving individual genomes.

Proper citation: SqueezeMeta (RRID:SCR_021821) Copy   

•   Source: SciCrunch Registry

https://circexplorer2.readthedocs.io/en/latest/

Software package for comprehensive and integrative circular RNA analysis. It is the successor of CIRCexplorer with plenty of new features to facilitate circular RNA identification and characterization. Used to annotate circRNAs, de novo assemble novel circular RNA transcripts and chracterize various of alternative (back-)splicing events of circular RNAs.

Proper citation: CIRCexplorer2 (RRID:SCR_021664) Copy   

•   Source: SciCrunch Registry

https://cumulus.readthedocs.io/en/stable

Software tool as cloud based single cell genomics and spatial transcriptomics data analysis framework that is scalable to massive amounts of data and able to process variety of data types. Consists of cloud analysis workflow, Python analysis package and visualization application. Supports analysis of single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire and spatial transcriptomics data.

Proper citation: Cumulus (RRID:SCR_021644) Copy   

•   Source: SciCrunch Registry

https://github.com/ANGSD/angsd

Software tool fo analysis of next generation sequencing data. Calculates various summary statistics, and performs association mapping and population genetic analyses utilizing full information in next generation sequencing data by working directly on raw sequencing data or by using genotype likelihoods.

Proper citation: ANGSD (RRID:SCR_021865) Copy   

•   Source: SciCrunch Registry

https://elucidata.io/el-maven/

Open source LC-MS data processing engine for simplifying metabolomics analysis. Mass spectrometry data processing engine that is optimal for isotopomer labeling and global metabolomic profiling experiments. Interactive software platform that accelerates analysis of LC-MS, GC-MS, and LC-MS/MS datasets.

Proper citation: EL MAVEN (RRID:SCR_022159) Copy   

•   Source: SciCrunch Registry

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

Software R package for cell type deconvolution of heterogeneous tissues based on bulk RNAseq data or single cell RNAseq expression profiles.Provides unified testing interface to rapidly run and benchmark multiple deconvolution methods.

Proper citation: granulator (RRID:SCR_022158) Copy   

•   Source: SciCrunch Registry

https://github.com/mourisl/Rcorrector

Software tool as kmer based error correction method for RNAseq data. Can also be applied to other types of sequencing data where read coverage is nonuniform, such as single cell sequencing. Used for error correction for Illumina RNAseq reads.

Proper citation: Rcorrector (RRID:SCR_022011) Copy   

•   Source: SciCrunch Registry

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

Software R package for statistical analysis of mixed ploidy populations.Used for calculation of population structure and differentiation based on single nucleotide polymorphism genotype data from populations of any ploidy level, and/or mixed ploidy levels.

Proper citation: StAMPP (RRID:SCR_022022) Copy   

•   Source: SciCrunch Registry

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

Software R package for estimation and tests of hierarchical F statistics.Used to estimate hierarchical F-statistics from haploid or diploid genetic data with any numbers of levels in hierarchy.Intended for analysis of population structure using genetic markers.

Proper citation: hierfstat (RRID:SCR_022021) Copy   

•   Source: SciCrunch Registry

http://cmpg.unibe.ch/software/BayeScan/index.html

Software tool to identify candidate loci under natural selection from genetic data, using differences in allele frequencies between populations.

Proper citation: BayeScan (RRID:SCR_022018) Copy   

•   Source: SciCrunch Registry

https://github.com/deeptools/HiCExplorer

Software tool to analyse Hi-C and capture Hi-C data. Command line suite of tools to process, normalize and visualize Hi-C data.

Proper citation: HiCExplorer (RRID:SCR_022111) Copy   

•   Source: SciCrunch Registry

https://frostconcepts.org/LeastBridgesGraphs/

Software tool as freely distributed computational method for analyzing distance relationships.

Proper citation: Least Bridges Graphs Mathematica package (RRID:SCR_022115) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/BASiCS/

Software tool for Bayesian analysis of single cell sequencing data. Used to perform statistical analyses of single cell RNA sequencing datasets in context of supervised experiments.

Proper citation: Bayesian Analysis of Single Cell Sequencing (RRID:SCR_021829) 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://ntap.cbi.pku.edu.cn/usage.php

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for tiling array data analysis to survey the genome-wide binding sites of transcription factor HY5 in Arabidopsis and the genome-wide histone modifications/DNA methylation level in rice. It was developed in the process of generating NimbleGen analysis. Written in R and Perl.

Proper citation: NTAP (RRID:SCR_001488) Copy   

•   Source: SciCrunch Registry

https://www.biodiscovery.com/search/node?keys=Imagene

Software tool as convolutional neural network to quantify natural selection from genomic data.Supervised machine learning algorithm to predict natural selection and estimate selection coefficients from population genomic data. Can be used to estimate any parameter of interest from evolutionary population genetics model., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ImaGene (RRID:SCR_002178) Copy   

•   Source: SciCrunch Registry

https://github.com/rajewsky-lab/spacemake

Software pipeline for processing and analysis of large scale spatial transcriptomics data. Enables reproducible data processing from raw sequencing data to automatically generated downstream analysis reports.

Proper citation: Spacemake (RRID:SCR_022207) Copy   

•   Source: SciCrunch Registry