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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://github.com/cancerit/cgpPindel
Software tool as cancer genome project insertion or deletion detection workflow for Pindel.
Proper citation: cgpPindel (RRID:SCR_017090) Copy
https://github.com/davidemms/OrthoFinder
Software Python application for comparative genomics analysis. Finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of gene duplcation events in those gene trees, infers rooted species tree for species being analysed and maps gene duplication events from gene trees to branches in species tree, improves orthogroup inference accuracy. Runs set of protein sequence files, one per species, in FASTA format.
Proper citation: OrthoFinder (RRID:SCR_017118) Copy
https://github.com/mikelove/tximport
Software R package for importing pseudoaligned reads into R for use with downstream differential expression analysis. Used for import and summarize transcript level estimates for transcript and gene level analysis.
Proper citation: tximport (RRID:SCR_016752) Copy
http://psych.colorado.edu/~lharvey/html/software.html
Software that fits s-shaped psychometric functions to psychophysical data using a maximum-likelihood technique. The psychometric functions available are logistic, Weibull, Gaussian integral, cumulative Poisson and step. PsychoFit produces, among other things, files with graphic information suitable for importing in a graphic program for plotting., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: PsychoFit (RRID:SCR_015381) Copy
https://github.com/zburkett/VoICE
Software that groups vocal elements of birdsong by creating a high dimensionality dataset through scoring spectral similarity between vocalizations.
Proper citation: Vocal Inventory Clustering Engine (VoICE) (RRID:SCR_016004) Copy
https://www.bioconductor.org/packages/release/bioc/html/MetaNeighbor.html
Software package to assess cell type identity using both functional and random gene sets. Used for single cell replicability analysis to quantify cell type replicability across datasets using neighbor voting.
Proper citation: MetaNeighbor (RRID:SCR_016727) Copy
Software that analyzes intestinal microbiota data. This environment is composed of a framework to process and analyze microbiota data from raw sequences to taxonomic and functional assignations.
Proper citation: ASaiM (RRID:SCR_015878) Copy
https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#bewith
Software tool for discovering relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions.
Proper citation: BeWith (RRID:SCR_016573) Copy
https://glimmpse.samplesizeshop.org/#/
Web based software tool that calculates power and sample size for study designs with normally distributed outcomes. Permits power calculations for clinical trials, randomized experiments, and observational studies with clustering, repeated measures, and both, and almost any testable hypothesis. GLIMMPSE Version 3 release back end has been refactored in Python, interface has been simplified, requiring user decisions about only one topic per screen, new menu improves specification of both between-participant and within-participant hypothese, recursive algorithm permits computing covariances for up to ten levels of clustering., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: GLIMMPSE (RRID:SCR_016297) Copy
https://github.com/sreeramkannan/Shannon
Software tool for de novo transcriptome assembly from RNA-Seq data.
Proper citation: Shannon (RRID:SCR_017037) Copy
https://github.com/ANGSD/ngsRelate
Software tool for estimating pairwise relatedness from next-generation sequencing data.
Proper citation: ngsRelate (RRID:SCR_016588) Copy
https://github.com/dfguan/purge_dups
Software tool to purge haplotigs and overlaps in assembly based on read depth.Used for haplotypic duplication identification. Designed to remove haplotigs and contig overlaps in a de novo assembly based on read depth.
Proper citation: purge dups (RRID:SCR_021173) Copy
https://github.com/hahnlab/CAFExp
Software tool for computational analysis of gene family evolution. Used for statistical analysis of evolution gene family sizes. Models evolution of gene family sizes over phylogeny.
Proper citation: Computational Analysis of gene Family Evolution (RRID:SCR_018924) Copy
https://github.com/theislab/scanpy
Software Python tool for large scale single cell gene expression data analysis. Integrates analysis possibilities of established R-based frameworks, provides pre processing, visualization, graph-drawing and diffusion maps, clustering, identification of marker genes for clusters via differential expression tests and pseudo temporal ordering via diffusion pseudo time.
Proper citation: scanpy (RRID:SCR_018139) Copy
https://gitlab.com/alexmascension/triku
Software tool as feature selection method based on nearest neighbors for single-cell data.
Proper citation: triku (RRID:SCR_020977) Copy
https://github.com/broadinstitute/Drop-seq
Software Java tools for analyzing Drop-seq data. Used to analyze gene expression from thousands of individual cells simultaneously. Analyzes mRNA transcripts while remembering origin cell transcript.
Proper citation: Drop-seq tools (RRID:SCR_018142) Copy
https://github.com/lkmklsmn/DrivAER
Software tool as method for identification of driving transcriptional programs based on AutoEncoder derived Relevance scores. Infers relevance scores for transcriptional programs with respect to specified outcomes of interest in single-cell RNA sequencing data, such as psuedotemporal ordering or disease status.Used for manifold interpretation in scRNA-seq data.
Proper citation: DrivAER (RRID:SCR_019076) Copy
https://github.com/gtonkinhill/panaroo
Software pipeline for pangenome investigation. Shares information between genomes to correct errors. Can call large structural variants.Fast and scalable to over 10k bacterial genomes.
Proper citation: Panaroo (RRID:SCR_021090) Copy
https://github.com/neurostuff/NiMARE
Software Python package for coordinate and image based meta analysis of neuroimaging data.
Proper citation: NiMARE (RRID:SCR_017398) Copy
https://shimadzu.com.au/labsolutions
Software package for data analysis by Shimadzu Oceania.
Proper citation: LabSolutions (RRID:SCR_018241) Copy
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