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https://majiq.biociphers.org/

Software package to detect and quantify local splicing variations (LSV) from RNA-Seq data. Used to automatically detect and downweight outliers in RNA-Seq datasets with replicates for differential splicing (SD) analysis.

Proper citation: MAJIQ (RRID:SCR_016706) Copy   

•   Source: SciCrunch Registry

http://odc-sci.org

Portal for sharing spinal cord injury data from basic and clinical research to promote transparency, rigor and reproducibility. Community based repository for spinal cord injury research.

Proper citation: Open Data Commons for Spinal Cord Injury (RRID:SCR_016673) Copy   

•   Source: SciCrunch Registry

https://github.com/CPernet/brain_colours

Software tool as a perceptually uniform color maps. Used in scientific literature to reflect data of brain imaging.

Proper citation: Colour maps for brain imaging (RRID:SCR_016715) 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://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://github.com/xia-lab/MetaboAnalystR

Software R package for comprehensive analysis of metabolomics data. Contains the R functions and libraries underlying MetaboAnalyst web server, including functions for metabolomic data analysis, visualization, and functional interpretation.

Proper citation: MetaboAnalystR (RRID:SCR_016723) Copy   

•   Source: SciCrunch Registry

https://www.agilent.com/en/products/software-informatics/masshunter-suite/masshunter-qualitative-analysis-gcms

Software tools for compound-centric data mining and navigation. Used to identify compounds in overlapping and co-eluting peaks with feature extraction and correlation algorithms for chromatographic separation. Used for separating true signals from noise.

Proper citation: Agilent MassHunter WorkStation - Qualitative Analysis for GC/MS (RRID:SCR_016657) 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://software.broadinstitute.org/gatk/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18th,2023. Software package for genome analysis. Used for analysis of next generation genomic data in cancer.

Proper citation: IndelGenotyper (RRID:SCR_016663) Copy   

•   Source: SciCrunch Registry

http://www.cbs.dtu.dk/biotools/sequenza/

Software package for copy number estimation from tumor genome sequencing data.Tools to analyze genomic sequencing data from paired normal-tumor samples, including cellularity and ploidy estimation; mutation and copy number (allele-specific and total copy number) detection, quantification and visualization.

Proper citation: Sequenza (RRID:SCR_016662) 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

https://github.com/vaklip/rsfmri_fconn

Software program for preprocessing resting state functional magnetic resonance imaging (rsfMRI) measurements and calculating region of interest based whole brain functional connectivity.

Proper citation: rsfMRI_fconn calculation (RRID:SCR_016591) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/Web/Search/entrezfs.html

Web portal for global query cross database search and retrieval system that provides access to all databases simultaneously with a single query string and user interface. Retrieves nucleotide and protein sequence data, gene centered and genomic mapping information, 3D structures, and references. Covers databases including protein sequence data from PIR-International, PRF, Swiss-Prot, and PDB and nucleotide sequence data from GenBank that includes information from EMBL and DDBJ.

Proper citation: Entrez (RRID:SCR_016640) 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://github.com/HussainiLab/hfoGUI

Graphical user interface to visualize EEG data. The applications can vary from scoring High Frequency Oscillations, to observing Theta and Gamma Synchrony.

Proper citation: hfoGUI (RRID:SCR_016726) 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://sleepdata.org/

System for sharing sleep data. Organization portal that aggregates, harmonizes, and organizes sleep and clinical data from individuals studied as part of cohort studies or clinical trials and provides suite of tools to facilitate data exploration and data visualization. National Heart, Lung, and Blood Institute resource designed to provide big data resources to sleep research community.

Proper citation: National Sleep Research Resource (NSRR) (RRID:SCR_016576) Copy   

•   Source: SciCrunch Registry

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

Software tool to provide color schemes for maps and other graphics. R package to create colorful graphs with pre-made color palettes that visualize data.

Proper citation: RColorBrewer (RRID:SCR_016697) Copy   

•   Source: SciCrunch Registry

http://ec2-52-91-98-53.compute-1.amazonaws.com/run/

Web based platform that integrates several bioinformatics tools for screening and annotation of cDNA construct sequences. Translates the nucleotide sequence of the construct into an amino acid sequence, aligns the predicted sequence to a reference database of protein sequences and identifies the best protein and isoform match, annotates any variants present in the construct, and incorporates disease-associated mutations and transcriptomic data.

Proper citation: Clonotator (RRID:SCR_016730) Copy   

•   Source: SciCrunch Registry

http://emg.nysbc.org/redmine/projects/leginon/wiki/Leginon_Homepage

System designed for automated collection of images from a transmission electron microscope.

Proper citation: Leginon (RRID:SCR_016731) Copy   

•   Source: SciCrunch Registry