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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/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
Software tool for a flow cytometry data analysis for Microsoft Windows enviroment developed by CyFlo Ltd. Has analysis capabilities, such as dot plot, histogram and statistics.
Proper citation: Cyflogic (RRID:SCR_016635) Copy
https://www.ncbi.nlm.nih.gov/sutils/pasc/viridty.cgi
Web tool for analysis of pairwise identity distribution within viral families. Used for virus sequence-based classification. Data in the system are updated every day to reflect changes in virus taxonomy and additions of new virus sequences to the public database.
Proper citation: PASC (RRID:SCR_016642) 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
http://home.cc.umanitoba.ca/~frist/Bit/
BIT Core at University of Manitoba, Manitoba, Canada, provides bioinformatics services, resources and collaborations. Support for Genome assembly and annotation, Microarray and Transcriptomics, Systems Biology and Pathway analysis, Databases, Data pipelines, Bioinformatics software, Custom software and programming, Project Wikis, Lab group computer management.
Proper citation: University of Manitoba Department of Plant Science Bio Information Technologies Lab Core Facility (RRID:SCR_017177) Copy
Community based, biologist friendly web platform for creating and meta analyzing annotated gene expression data compendia., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: OMiCC (RRID:SCR_016604) Copy
https://github.com/wilkinsonlab/epigenomics_pipeline
Software tool as epigenomics analysis pipeline for analysis of ChIP-Seq and RNA-Seq data using Docker images containing Galaxy and Jupyter.
Proper citation: Epigenomics Workflow on Galaxy and Jupyter (RRID:SCR_017544) Copy
Platform to provide tutorials and resources in experimental design and data analysis to researchers interested in using optical mapping data.
Proper citation: OpticalMapping.info (RRID:SCR_017146) Copy
https://cran.r-project.org/web/packages/factoextra/index.html
R package from CRAN to extract and visualize the results of multivariate data analysis.
Proper citation: factoextra (RRID:SCR_016692) 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://www.iconplc.com/innovation/nonmem/
Software tool for nonlinear mixed effects modelling. Used for population pharmacokinetic and pharmacodynamic analysis and to simulate data and to fit data. Used in the development of new drugs. NONMEM versions up through 6 are the property of the Regents of the University of California, San Francisco, but ICON Development Solutions has exclusive rights to license their use. NONMEM 7 up to the current version is the property of ICON Development Solutions.
Proper citation: NONMEM (RRID:SCR_016986) Copy
https://github.com/satijalab/seurat
Software R package designed for QC, analysis, and exploration of single cell RNA-seq data. Enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. Used for quality control, analysis, and exploration of single-cell RNA sequencing (scRNA-seq) data.
Proper citation: Seurat (RRID:SCR_016341) Copy
http://www.imgt.org/HighV-QUEST/home.action
Next generation B and T cell sequence alignment and characterization online surface by IMGT. Web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing.
Proper citation: IMGT HighV-QUEST (RRID:SCR_018196) Copy
Software tool for statistics and data visualization by Red Rock Software, Inc. Provides unparalleled chart selection, data analysis and graph customization capabilities.
Proper citation: Deltagraph (RRID:SCR_018084) Copy
http://shiny.chemgrid.org/boxplotr/
Web tool written in R for generation of box plots with R packages shiny, beanplot4, vioplot, beeswarm and RColorBrewer, and hosted on shiny server to allow for interactive data analysis. Data are held temporarily and discarded as soon as session terminates.Represents both summary statistics and distribution of primary data. Enables visualization of minimum, lower quartile, median, upper quartile and maximum of any data set.Data matrix can be uploaded as file or pasted into application. May be downloaded to run locally or as virtual machine for VMware and VirtualBox.
Proper citation: BoxPlotR (RRID:SCR_015629) Copy
https://genome.tugraz.at/genesisclient/genesisclient_description.shtml
Software for cluster analysis of microarray data. Genesis is a platform independent Java package of tools to simultaneously visualize and analyze a whole set of gene expression experiments.
Proper citation: Genesis (RRID:SCR_015775) Copy
https://github.com/DDTBOX/DDTBOX
Software toolkit for multivariate pattern analysis (MVPA) of event-related potentials. This software is written in MATLAB.
Proper citation: Decision Decoding Toolbox (RRID:SCR_015978) Copy
Software for semantic chemical editing, visualization, and analysis. It is designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
Proper citation: Avogadro (RRID:SCR_015983) Copy
https://github.com/sanger-pathogens/Bio-Tradis
Analysis software for the output from TraDIS (Transposon Directed Insertion Sequencing) analyses of dense transposon mutant libraries. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools.
Proper citation: Bio-tradis (RRID:SCR_015993) Copy
https://github.com/EvolBioInf/andi
Software tool for rapidly computing and estimating evolutionary distance between closely related genomes. Because andi does not compute full alignments it scales even up to thousands of bacterial genomes.
Proper citation: andi (RRID:SCR_015971) Copy
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