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http://research.mssm.edu/integrative-network-biology/Software.html

Software tool as probabilistic multi omics data matching procedure to curate data, identify and correct data annotation and errors in large databases. Used to check potential labeling errors in profiles where number of cis relationships is small, such as miRNA and RPPA profiles.

Proper citation: proMODMatcher (RRID:SCR_017219) Copy   

•   Source: SciCrunch Registry

https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger

Software tool as set of analysis pipelines that process chromium single cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis by 10xGenomics.

Proper citation: Cell Ranger (RRID:SCR_017344) Copy   

•   Source: SciCrunch Registry

https://github.com/aidenlab/juicer.git

Software platform for analyzing kilobase resolution Hi-C data. Open source tool for analyzing terabase scale Hi-C datasets. Allowes to transform raw sequence data into normalized contact maps.

Proper citation: Juicer (RRID:SCR_017226) Copy   

•   Source: SciCrunch Registry

http://snf-515788.vm.okeanos.grnet.gr/

Web tool for integrating human and mouse microRNAs in pathways.Pathway analysis web-server, providing statistics, while being able to accommodate advanced pipelines. Web server for assessment of miRNA regulatory roles and identification of controlled pathways. Supports all analyses for KEGG molecular pathways and Gene Ontology (GO) in seven species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Caenorhabditis elegans, Gallus gallus and Danio rerio).DIANA miRPath v.2.0 includes investigating combinatorial effect of microRNAs in pathways.DIANA-miRPath v3.0 includes deciphering microRNA function with experimental support., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: DIANA-mirPath (RRID:SCR_017354) Copy   

•   Source: SciCrunch Registry

http://pathwaynet.princeton.edu/

Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks.

Proper citation: PathwayNet (RRID:SCR_017353) Copy   

•   Source: SciCrunch Registry

https://www.keyence.co.jp/products/microscope/fluorescence-microscope/bz-8100/models/bz-h1a/

Software tool as analysis application BZ-H1A by Keyence, Japan for fluorescence microscope BZ-8100 series.

Proper citation: BZ Analyzer software (RRID:SCR_017205) Copy   

•   Source: SciCrunch Registry

http://relacs.sourceforge.net/

Software platform for closed loop data acquisition, online analysis, and stimulus generation specifically designed for, but not limited to, electrophysiological recordings.

Proper citation: Relacs (RRID:SCR_017280) Copy   

•   Source: SciCrunch Registry

https://www.mbfbioscience.com/vesselucida360

Software tool for visualization and automatic reconstruction of microvascular networks in 3D environment with built-in analysis tools by MBF Bioscience.

Proper citation: Vesselucida 360 (RRID:SCR_017320) Copy   

•   Source: SciCrunch Registry

http://trimal.cgenomics.org/

Software tool for automated removal of spurious sequences or poorly aligned regions from multiple sequence alignment. Software package for automated alignment trimming in large scale phylogenetic analyses.

Proper citation: trimAl (RRID:SCR_017334) Copy   

•   Source: SciCrunch Registry

https://arxiv.org/abs/1308.2012

Software tool for estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects. Used as general and assembly independent method for estimating genomic characteristics.

Proper citation: GCE (RRID:SCR_017332) Copy   

•   Source: SciCrunch Registry

https://www.beckman.fr/flow-cytometry/instruments/cytoflex/software

Software program that controls instrument operation, data collection and analysis. Software for CytoFLEX Platform by Beckman Coulter.

Proper citation: CytExpert Software (RRID:SCR_017217) Copy   

•   Source: SciCrunch Registry

https://github.com/EpistasisLab/pennai

Open source software tool to leverage supervised machine learning techniques to analyze data. Can assist with tasks such as choosing appropriate models for data. Data science assistant for generating results from large and complex data problems.

Proper citation: PennAI (RRID:SCR_017215) Copy   

•   Source: SciCrunch Registry

https://www.cmrr.umn.edu/downloads/mrspa

Software package to post process MR spectroscopy data. Magnetic Resonance signal processing and analysis software. Runs under Matlab.

Proper citation: MRspa (RRID:SCR_017292) Copy   

•   Source: SciCrunch Registry

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

Software package for interactive graphics for gene expression analysis. Generates interactive visualisations for analysis of RNA-sequencing data.

Proper citation: Glimma (RRID:SCR_017389) Copy   

•   Source: SciCrunch Registry

https://www.beast2.org/

Software package for advanced Bayesian evolutionary analysis by sampling trees. Used for phylogenetics, population genetics and phylodynamics. Program for Bayesian phylogenetic analysis of molecular sequences. Estimates rooted, time measured phylogenies using strict or relaxed molecular clock models. Framework can be extended by third parties. Comprised of standalone programs including BEAUti, BEAST, MASTER, RBS, SNAPP, MultiTypeTree, BDSKY, LogAnalyser, LogCombiner, TreeAnnotator, DensiTree and package manager.

Proper citation: BEAST2 (RRID:SCR_017307) Copy   

•   Source: SciCrunch Registry

https://github.com/ISUgenomics/SequelQC

Software tool that calculates key statistics and generates publication quality plots for raw PacBio Sequel data. Open source software for analyzing PacBio Sequel raw sequence data.

Proper citation: SequelQC (RRID:SCR_017279) Copy   

•   Source: SciCrunch Registry

https://www.qtiplot.com/

Software tool for data analysis and scientific visualization by IONDEV SRL.

Proper citation: QtiPlot (RRID:SCR_017311) Copy   

•   Source: SciCrunch Registry

http://www.bioisis.net

Software JAVA based application for basic analysis of Small Angle X-ray Scattering datasets.

Proper citation: SCÅTTER (RRID:SCR_017271) Copy   

•   Source: SciCrunch Registry

https://depmap.org/portal/

Portal for identifying genetic and pharmacologic dependencies and biomarkers that predicts them by providing access to datasets, visualizations, and analysis tools that are being used by Cancer Dependency Map Project at Broad Institute. Project to systematically identify genes and small molecule dependencies and to determine markers that predict sensitivity. All data generated by DepMap Project are available to public under CC BY 4.0 license on quarterly basis and pre-publication.

Proper citation: Cancer Dependency Map Portal (RRID:SCR_017655) Copy   

•   Source: SciCrunch Registry

https://deepblue.mpi-inf.mpg.de/

Central data access hub for large collections of epigenomic data. It organizes data from different sources using controlled vocabularies and ontologies. Data Server for storing, organizing, searching, and retrieving genomic and epigenomic data, handling associated metadata, and to perform different types of analysis.

Proper citation: Deep Blue Epigenomic Data Server (RRID:SCR_017490) Copy   

•   Source: SciCrunch Registry