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http://www.nitrc.org/projects/psc/

Data analysis software that can simultaneously characterize a large number of white matter bundles within and across different subjects for group analysis. It has three major components: construction of the structural connectome for the whole brain, low-dimensional representation of streamlines in each connection, and multi-level connectome analysis.

Proper citation: Mapping Population-based Structural Connectomes (RRID:SCR_016232) Copy   

•   Source: SciCrunch Registry

https://www.hiv.lanl.gov/catnap

Analyze a database of HIV-1 IC50 and IC80 neutralization data from publicly-available sources, in conjunction with HIV-1 Envelope sequences. Access to an extensive databases of information about neutralizing antibodies and viruses used in published neutralization studies. Tool interfaces also allow input and analysis of user data. PMID: 26044712, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CATNAP (RRID:SCR_016170) Copy   

•   Source: SciCrunch Registry

https://www.denovosoftware.com/?gclid=EAIaIQobChMI36rn3-Dd3AIV2ud3Ch27lw2oEAAYASAAEgLbRvD_BwE

Software tool for flow and image cytometry data analysis by De Novo Software company.

Proper citation: FCS Express (RRID:SCR_016431) Copy   

•   Source: SciCrunch Registry

https://www.genomics.agilent.com/article.jsp?pageId=2100

Software that performs data analysis algorithms for QPCR data. The software is included with the purchase of the Agilent MxPro QPCR System., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MxPro QPCR (RRID:SCR_016375) Copy   

•   Source: SciCrunch Registry

https://niaid.github.io/dcas/

Web tool to import raw cDNA sequences, clean sequences, build sequence contigs, perform SignalP analysis, BLAST contigs against numerous BLAST databases, and view the results. Automates large scale cDNA sequence analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: dCAS (RRID:SCR_016612) Copy   

•   Source: SciCrunch Registry

https://www.uamh.ca/

Repository of microbial in Canada. Culture collection, preservation, analysis, identification of fungi living strains. Backed up by herbarium dried colonies. A reference and training centre for the identification of human and animal pathogens and allied taxa.Provides advice or assistance to projects involving fungi.

Proper citation: UAMH Centre for Global Microfungal Biodiversity (RRID:SCR_016466) Copy   

•   Source: SciCrunch Registry

https://github.com/tomazc/iCount

Software Python package for protein-RNA interaction analysis. Used for analysis of protein-RNA interactions with iCLIP sequencing data and RNA maps.

Proper citation: iCount (RRID:SCR_016712) Copy   

•   Source: SciCrunch Registry

https://github.com/Crick-CancerGenomics/ascat

Software R package to infer tumor purity, ploidy and allele-specific copy number profiles. It is platform and species independent, and works for both Illumina and Affymetrix SNP arrays, as well as for massively parallel sequencing data.

Proper citation: ascat (RRID:SCR_016868) Copy   

•   Source: SciCrunch Registry

https://github.com/aroth85/pyclone

Software tool to infer the prevalence of point mutations in heterogeneous cancer samples. Probabilistic model for inferring clonal population structure from deep NGS sequencing.

Proper citation: Pyclone (RRID:SCR_016873) Copy   

•   Source: SciCrunch Registry

https://github.com/kendomaniac/rCASC

Software package for reproducible classification analysis of single cell sequencing data.

Proper citation: rCASC (RRID:SCR_017005) Copy   

•   Source: SciCrunch Registry

https://eda.nc3rs.org.uk/

Web based tool to help in vivo researchers improve design, conduct, analysis and reporting of animal experiments.Provides automated feedback on proposed design and generates graphical summary that aids communication with colleagues, founders and regulatory authorities. Addresses causes of irreproducibility.

Proper citation: Experimental Design Assistant (RRID:SCR_017019) Copy   

•   Source: SciCrunch Registry

https://github.com/ToolsVanBox/smMIPfil

Software tool for single molecule Molecular Inversion Probes data analysis. This is a stand-alone perl script. Except that this is dependent on the samtools, no installation required.

Proper citation: smMIPfil (RRID:SCR_016892) Copy   

•   Source: SciCrunch Registry

https://github.com/nolanlab/VORTEX

Software Java graphical tool for single cell analysis, clustering and visualization. Provides multithreaded implementations of clustering algorithms, including nonparametric density based X shift, Hierarchical clustering, Mean shift and K medoids.

Proper citation: VORTEX (RRID:SCR_017047) Copy   

•   Source: SciCrunch Registry

https://github.com/dpeerlab/phenograph

Software tool as clustering method designed for high dimensional single cell data. Algorithmically defines phenotypes in high dimensional single cell data. Used for large scale analysis of single cell heterogeneity.

Proper citation: Phenograph (RRID:SCR_016919) Copy   

•   Source: SciCrunch Registry

https://github.com/Frederik-D-Weber/cosleep

Software Python tool for sleep EEG analysis. Used for Closed and Open loop in Slow Ocillations, Sleep Stimulation in Auditory or Recording in full PSG using OpenBCI Cyton.

Proper citation: COsleep (RRID:SCR_017053) Copy   

•   Source: SciCrunch Registry

https://sedfitsedphat.nibib.nih.gov/software/default.aspx

Software tool for analytical ultracentrifugation developed by Dynamics of Macromolecular Assembly group of Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, NIH. Used for biophysical analysis of macromolecular assembly.

Proper citation: SEDFIT (RRID:SCR_018365) Copy   

•   Source: SciCrunch Registry

http://www.fsm.ethz.ch/publications-list/software.html

Software for tracking and analysis based on algorithms describing structural and topological features of fiber-like objects. The program operates on images from any microscopic source (atomic force or transmission electron microscopy, optical, fluorescence, confocal, etc.), acquiring the spatial coordinates of objects.

Proper citation: FiberApp (RRID:SCR_015826) Copy   

•   Source: SciCrunch Registry

https://github.com/harry-thorpe/piggy

Pipeline for analyzing intergenic regions in bacteria. It is designed to be used in conjunction with Roary (https://github.com/sanger-pathogens/Roary).

Proper citation: Piggy (RRID:SCR_015941) Copy   

•   Source: SciCrunch Registry

https://github.com/neurodroid/stimfit

Software for viewing and analyzing electrophysiological data. It features an embedded Python shell that allows you to extend the program functionality by using numerical libraries such as NumPy and SciPy.

Proper citation: Stimfit (RRID:SCR_016050) Copy   

•   Source: SciCrunch Registry

https://github.com/Rinoahu/SwiftOrtho

Software tool for orthology analysis to identify orthologs, paralogs and co orthologs for genomes. Used to perform homology classification across genomes of different species in large genomic datasets.

Proper citation: SwiftOrtho (RRID:SCR_017122) Copy   

•   Source: SciCrunch Registry