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http://saclab.tamu.edu/essentiality/transit/

Software tool Python based and open source for statistical analysis of TnSeq data. Provides a graphical interface to three different statistical methods for analyzing TnSeq data capable of identifying essential genes in individual datasets as well as comparative analysis between conditions.

Proper citation: TRANSIT (RRID:SCR_016492) Copy   

•   Source: SciCrunch Registry

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

Software R package as a nonparametric statistical test to compare clustering structures with applications in functional magnetic resonance imaging data (fMRI). Used for analysis of cluster variability in the diagnosis of neuropsychological disorders.

Proper citation: ANOCVA (RRID:SCR_016719) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/geo/info/geo2r.html

Software as an interactive web tool to compare two or more groups of samples in a Gene Expression Omnibus (GEO) series regardless of data type and quality. Used to identify genes that are differentially expressed across experimental conditions. Results are presented as a table of genes ordered by significance.

Proper citation: GEO2R (RRID:SCR_016569) Copy   

•   Source: SciCrunch Registry

https://card.niaid.nih.gov

Web application for integrated analysis and interactive visualization of RNA interference (RNAi) screening data.

Proper citation: CARD (RRID:SCR_016602) Copy   

•   Source: SciCrunch Registry

https://visrsoftware.github.io/

Software as an R-based visual framework for analysis of sequencing datasets. Provides a framework for integrative and interactive analyses.

Proper citation: VisR (RRID:SCR_016658) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/biobakery/biobakery/wiki/Home

Analysis environment and collection of individual software tools to process raw shotgun metagenome or metatranscriptome sequencing data for quantitative microbial community profiling. Used for a metaomics data analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: biobakery (RRID:SCR_016596) Copy   

•   Source: SciCrunch Registry

http://phenomenal-h2020.eu/

Cloud based standardised European e-infrastructure for metabolomics and phenomics data processing, analysis and information mining on public or private cloud providers. Used for large scale computing for medical metabolomics.

Proper citation: PhenoMeNal (RRID:SCR_016605) Copy   

•   Source: SciCrunch Registry

https://niaid.github.io/spice/

Software application for data mining and visualization. Used for analyzes of large FLOWJO data sets from polychromatic flow cytometry and organizing the normalized data graphically.

Proper citation: SPICE (RRID:SCR_016603) Copy   

•   Source: SciCrunch Registry

https://www.omicsnet.ca/

Web based tool to create different types of molecular interaction networks and visually explore them in a three-dimensional (3D) space (genes/proteins, microRNAs, transcription factors or metabolites).

Proper citation: OmicsNet (RRID:SCR_016724) Copy   

•   Source: SciCrunch Registry

http://scipion.i2pc.es/

Software framework for image processing to obtain 3D models of macromolecular complexes using Electron Microscopy. Open-source project for integration, reproducibility and validation in 3D electron microscopy. It integrates several software packages to execute workflows combining different software tools, while taking care of formats and conversions. Electron Microscopy (3DEM). waiting for pdf from Joe

Proper citation: SCIPION (RRID:SCR_016738) Copy   

•   Source: SciCrunch Registry

http://metascape.org/gp/index.html#/main/step1

Web service to analyze gene or protein lists. Provides automated meta analysis tools to understand pathways within a group of orthogonal target-discovery studies.

Proper citation: Metascape (RRID:SCR_016620) Copy   

•   Source: SciCrunch Registry

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

Software R package for sequence alignment and counting for R. Used for analyses of second and third generation sequencing data, for read mapping, read counting, SNP calling, short and long read alignment, quantification and mutation discovery. Includes assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers.

Proper citation: Rsubread (RRID:SCR_016945) Copy   

•   Source: SciCrunch Registry

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

Software package for low-level analyses of single-cell RNA-seq data. Used for quality control, data exploration and normalization, cell cycle phase assignment, identification of highly variable and correlated genes, clustering into subpopulations and marker gene detection.

Proper citation: scran (RRID:SCR_016944) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/ConsensusClusterPlus.html

Software written in R for determining cluster count and membership by stability evidence in unsupervised analysis. Provides quantitative and visual stability evidence for estimating the number of unsupervised classes in a dataset with item tracking, item consensus and cluster consensus plots.

Proper citation: ConsensusClusterPlus (RRID:SCR_016954) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/GenomicFeatures/

Software R package for making and manipulating transcript centric annotations. Used to download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database.

Proper citation: GenomicFeatures (RRID:SCR_016960) Copy   

•   Source: SciCrunch Registry

https://biii.eu/

Web platform for bio image analysis. Used to share knowledge between the different communities, to help biologists to find any tool or workflow available for a particular image analysis problem and to find the adequate image processing wording, to help software and algorithm developers to find missing tools (or components), and to help bioimage analyst to identify and edit workflows.

Proper citation: BISE (RRID:SCR_016774) Copy   

•   Source: SciCrunch Registry

https://github.com/SofieVG/FlowSOM

Software tool to analyze Flow or mass cytometry data using a Self-Organizing Map. Used to obtain an overview of how all markers are behaving on all cells, and to detect subsets that might be missed otherwise.

Proper citation: FlowSOM (RRID:SCR_016899) Copy   

•   Source: SciCrunch Registry

https://github.com/OpenSMFS/FRETBursts

Software for burst analysis of freely diffusing single-molecule Förster Resonance Energy Transfer (smFRET) experiments to study cellular processes at the molecular scale. Used for single and multi-spot single-molecule FRET (smFRET) data.

Proper citation: FRETBursts (RRID:SCR_016898) Copy   

•   Source: SciCrunch Registry

https://github.com/qiicr/dcmqi

Software library to help with the conversion between imaging research formats and the standard DICOM representation for image analysis results. Used to implement conversion of the data stored in commonly used research formats into the standard DICOM representation. Available as a precompiled binary package for every major operating system, as a Docker image, and as an extension to 3D Slicer.

Proper citation: dcmqi (RRID:SCR_016933) Copy   

•   Source: SciCrunch Registry

https://www.networkanalyst.ca/

Web tool for gene expression profiling, meta-analysis and systems understanding. Used for statistical, visual and network-based meta-analysis of gene expression data.

Proper citation: NetworkAnalyst (RRID:SCR_016909) Copy   

•   Source: SciCrunch Registry