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http://starbase.sysu.edu.cn/index.php

Web based tool to visualize, analyze, discover and download of large-scale functional genomics data. Used for analysis of the CLIP-Seq and Degradome-Seq data sets, exploration of miRNA–target interactions and decoding RNA interaction networks from CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) data. To show RNA-RNA and protein-RNA interaction networks in developmental, physiological and pathological processes.

Proper citation: Starbase V2.0 (RRID:SCR_016303) Copy   

•   Source: SciCrunch Registry

https://fractalis.lcsb.uni.lu/

Software as a scalable open-source service for platform-independent interactive visual analysis of biomedical data. It is a service and a library that work in tandem to equip existing platforms with visual analytical capabilities for explorative data analysis.

Proper citation: Fractalis (RRID:SCR_016362) Copy   

•   Source: SciCrunch Registry

https://github.com/lanagarmire/lilikoi

Software tool as an R package for personalized pathway-based classification modeling using metabolomics data. Provides personalized pathway deregulation measurements (PDS scores) and offers a standardized classification model for biomarker prediction.

Proper citation: lilikoi (RRID:SCR_016361) Copy   

•   Source: SciCrunch Registry

https://www.pbcconsortium.org/

Portal to provide a repository for beta-cell data, to connect researchers from different backgrounds interested in contributing data, models and/or ideas for new insights into beta-cell biology. Used to understand beta-cell biology and diabetes through a cross-disciplinary approach for the assembly of spatiotemporal multi-scale whole cell models of human pancreatic beta-cells.

Proper citation: The Pancreatic Beta-Cell Consortium (RRID:SCR_016328) Copy   

•   Source: SciCrunch Registry

http://fmri.uib.no/index.php?option=com_content&view=article&id=53&Itemid=78

Software package as a set of Matlab tools which allow the correction of fMRI-related gradient artifacts from EEG data. Designed to work within the EEGLAB environment, providing a GUI to remove fMRI gradient artifacts from the EEG. Can also be used from the Matlab command line, providing expert users with the ability to use them in custom scripts.

Proper citation: The Bergen fMRI Toolbox Plugin for EEGLab (RRID:SCR_016335) Copy   

•   Source: SciCrunch Registry

http://cole-trapnell-lab.github.io/monocle-release/docs/

Software package for analyzing single cell gene expression, classifying and counting cells, performing differential expression analysis between subpopulations of cells, and reconstructing cellular trajcectories. Works well with very large single-cell RNA-Seq experiments containing tens of thousands of cells or more. Used in computational analysis of gene expression data in single cell gene expression studies to profile transcriptional regulation in complex biological processes and highly heterogeneous cell populations.

Proper citation: Monocle2 (RRID:SCR_016339) Copy   

•   Source: SciCrunch Registry

https://github.com/KM-Lab/Electrographic-Seizure-Analyzer

Software to automate analysis of electrographic seizures based on EEG or LFP data, featuring customizable thresholds and parameters for event detection and parameter setting.

Proper citation: Electrographic Seizure Analyzer (RRID:SCR_016344) Copy   

•   Source: SciCrunch Registry

http://jvenn.toulouse.inra.fr/app/example.html

JavaScript plug-in software application for web environments to analyze data. It is an interactive Venn diagram viewer.Used for comparing lists with Venn Diagrams. It handles up to six input lists and presents results using classical or Edwards-Venn layouts. User interactions can be controlled and customized.

Proper citation: jVenn (RRID:SCR_016343) Copy   

•   Source: SciCrunch Registry

https://github.com/jkrijthe/Rtsne

Software as R wrapper for Van der Maaten's Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding. Used for high-dimentional data visualisation.

Proper citation: Rtsne (RRID:SCR_016342) Copy   

•   Source: SciCrunch Registry

https://amp.pharm.mssm.edu/biojupies/

Software as an open source web server that automatically generates RNA-seq data analysis of jupyter notebooks. It allows creation and containment of documents that have live code, visualizations and narrative text.

Proper citation: BioJupies (RRID:SCR_016346) Copy   

•   Source: SciCrunch Registry

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

Software as an open source package for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.

Proper citation: MAST (RRID:SCR_016340) Copy   

•   Source: SciCrunch Registry

https://www.myassays.com/

Software tool for assay data analysis.

Proper citation: MyAssays (RRID:SCR_016562) 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

http://bioinfogp.cnb.csic.es/tools/venny/

Software tool for comparing lists with Venn's diagrams.

Proper citation: Venny 2.1 (RRID:SCR_016561) Copy   

•   Source: SciCrunch Registry

https://omictools.com/splicing-express-tool

Software suite for Alternative Splicing Events (ASEs) analysis from transcriptome sequencing data in any transcriptome. Used for identification, annotation and visualization. Written in Perl and suitable to run only in UNIX-like systems.

Proper citation: Splicing Express (RRID:SCR_016498) Copy   

•   Source: SciCrunch Registry

https://github.com/PF2-pasteur-fr/SARTools

Software package as a DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data.

Proper citation: SARTools (RRID:SCR_016533) Copy   

•   Source: SciCrunch Registry

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

http://bioinformatics.mdc-berlin.de/pigx/

Software application as a collection of genomic pipelines used for raw fastq read data of bisulfite experiments, RNAseq samples, single cell dropseq analysis, reads from ChIPseq experiments, analysis of sequence mutations in CRISPR-CAS9 targeted amplicon sequencing data.

Proper citation: PiGx (RRID:SCR_016476) 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