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https://github.com/vetscience/Assemblosis

Software tool as a Common Workflow Language (CWL) based automated bioinformatics workflow to assemble haploid/diploid eukaryote genomes of non-model organisms using PacBio long-reads and Illumina short-reads.

Proper citation: Assemblosis (RRID:SCR_016571) Copy   

•   Source: SciCrunch Registry
  

https://lsbr.niams.nih.gov/bsoft/

Software package and a platform for the processing of electron micrographs in structural biology. Supports different image file formats used in electron microscopy (including MRC, SPIDER, IMAGIC, SUPRIM, and PIF)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Bsoft (RRID:SCR_016503) Copy   

•   Source: SciCrunch Registry
  

https://www.cabi.org/

An international not-for-profit organization to solve problems in agriculture and the environment. Specialize in microbial identification and verification, and provide professional microbiology services in support of industry, academia and agriculture. Established by a United Nations.

Proper citation: Centre for Agriculture and Biosciences International (RRID:SCR_016467) Copy   

•   Source: SciCrunch Registry
  

http://fusion.sph.umich.edu/

Portal to map and identify genetic variants that predispose to type 2 diabetes mellitus (T2D) or are responsible for variability in diabetes-related quantitative traits. Used for analysis of affected-sibling-pair (ASP) families in Finland, and association fine mapping based on these family members and additional T2D cases and controls.

Proper citation: FUSION study (RRID:SCR_016580) Copy   

•   Source: SciCrunch Registry
  

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

Software tool for working with data frame like objects, both in memory and out of memory. It is a grammar of data manipulation, providing a consistent set of verbs that help you solve the most common data manipulation challenges: mutate, select, filer, summerise, arrange.

Proper citation: dplyr (RRID:SCR_016708) Copy   

•   Source: SciCrunch Registry
  

http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html

Software tool as a framework for modeling the sequences of short sequence motifs based on the maximum entropy principle (MEP). Used for sequence motifs such as those involved in RNA splicing.

Proper citation: MAxEntScan (RRID:SCR_016707) Copy   

•   Source: SciCrunch Registry
  

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
  

http://microc.org

Software tool to model genotypes in their microenvironment and to predict single- and multi-cellular behaviour. A 3D virtual microenvironment for perturbation biology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: microC (RRID:SCR_016672) 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://github.com/farshidrayhanuiu/iDTI-ESBoost

Software tool for identification of Drug Target Interaction using Evolutionary and Structural features with Boosting. Used to predict drug-protein interactions.

Proper citation: iDTI-ESBoost (RRID:SCR_016720) Copy   

•   Source: SciCrunch Registry
  

https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_016647.pdf

Instrument for nanoparticle tracking analysis. A semi-automated method for the characterization of extracellular vesicles with associated analysis software by ParticleMetrix GmbH.

Proper citation: Particle Metrix: ZetaView Nanoparticle Tracking Analyzer (RRID:SCR_016647) 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://www.janelia.org/project-team/mouselight

Software imaging platform to generate datasets of whole mouse brains imaged at submicron resolution that allow reconstructions of complete axonal arbors of individual neurons across the entire mouse brain.

Proper citation: MouseLight Project (RRID:SCR_016668) Copy   

•   Source: SciCrunch Registry