Tools   Select Another Resource Report Type

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   

•   Source: SciCrunch Registry

http://ccg.vital-it.ch/snp2tfbs

Collection of text files providing specific annotations for human single nucleotide polymorphisms (SNPs), namely whether they are predicted to abolish, create or change the affinity of one or several transcription factor (TF) binding sites. Used to investigate the molecular mechanisms underlying regulatory variation in the human genome. SNP2TFBS is also accessible over a web interface, enabling users to view the information provided for an individual SNP, to extract SNPs based on various search criteria, to annotate uploaded sets of SNPs or to display statistics about the frequencies of binding sites affected by selected SNPs.

Proper citation: SNP2TFBS (RRID:SCR_016885) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://hpc-bioinformatics.cineca.it/stress_mice/

Sapienza University of Rome and Cineca consortium portal. Used for analyzing published RNAseq transcriptomes obtained from brain of mice exposed to different kinds of stress protocols, to generate database of stress related differentially expressed genes and to identify factors contributing to vulnerability or resistance to stress. Allows to query database of RNAseq data.

Proper citation: Stress Mice Portal (RRID:SCR_017572) Copy   

•   Source: SciCrunch Registry

https://omicc.niaid.nih.gov

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://opticalmapping.info

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/sreeramkannan/Shannon

Software tool for de novo transcriptome assembly from RNA-Seq data.

Proper citation: Shannon (RRID:SCR_017037) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/ANGSD/ngsRelate

Software tool for estimating pairwise relatedness from next-generation sequencing data.

Proper citation: ngsRelate (RRID:SCR_016588) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html

Software package to arrange multiple heatmaps and support various annotation graphics. Used to visualize associations between different sources of data sets and to reveal potential patterns.

Proper citation: ComplexHeatmap (RRID:SCR_017270) Copy   

•   Source: SciCrunch Registry

http://redrocksw.com/

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   

•   Source: SciCrunch Registry

https://satijalab.org/seurat/get_started.html

Software as 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.

Proper citation: Seurat (RRID:SCR_016341) Copy   

•   Source: SciCrunch Registry

http://sharedresources.fredhutch.org/core-facilities/bioinformatics

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 27,2022. Core provides bioinformatics specialists available to assist researchers with processing, exploring, and understanding genomics data.

Proper citation: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Bioinformatics Resource (RRID:SCR_015324) Copy   

•   Source: SciCrunch Registry

http://cerebrovascularportal.org

Portal enables browsing, searching, and analysis of human genetic information linked to cerebrovascular disease and related traits, while protecting the integrity and confidentiality of the underlying data.

Proper citation: Cerebrovascular Disease Knowledge Portal (RRID:SCR_015628) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://openneuro.org

Open platform for analyzing and sharing neuroimaging data from human brain imaging research studies. Brain Imaging Data Structure ( BIDS) compliant database. Formerly known as OpenfMRI. Data archives to hold magnetic resonance imaging data. Platform for sharing MRI, MEG, EEG, iEEG, and ECoG data.

Proper citation: OpenNeuro (RRID:SCR_005031) Copy   

•   Source: SciCrunch Registry