Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
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.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Washington University School of Medicine Genome Technology Access Center Core Facility Resource Report Resource Website 1+ mentions |
Washington University School of Medicine Genome Technology Access Center Core Facility (RRID:SCR_001030) | WUSTL GTAC, GTAC | service resource, access service resource, core facility | Genome Access Technology Center at the McDonnell Genome Institute offers comprehensive next generation sequencing, microarray, PCR and Bioinformatic services. In addition to generating high quality genomic, transcriptomic, and proteomic data, performs data analysis and provides technological support to users. Full service facility, from hypothesis to publication. Offers advanced analysis of microarray data. Provides free initial consultation to discuss project and offers several tiers of analysis packages to best suit your needs. NGS equipment includes NovaSeqs, Seqwell II, Oxford. Microarray expression and genotyping - all platforms. | Next generation sequencing, microarray, PCR, bioinformatic service, data analysis, ABRF, USEDit |
is listed by: ScienceExchange is listed by: ABRF CoreMarketplace is related to: Washington University in St. Louis School of Medicine Division of Biology and Biomedical Sciences has parent organization: Washington University in St. Louis; Missouri; USA |
Open | SCR_018204, SCR_018300, SciEx_32, ABRF_279 | https://coremarketplace.org/?FacilityID=279 | http://www.scienceexchange.com/facilities/genome-technology-access-center-gtac-wustl | SCR_001030 | Washington University McDonnell Genome Institute Genome Technology Access Center, , Genome Technology Access Center, Washington University School of Medicine GTAC Core Facility, Washington University in St. Louis Genome Technology Access Center, McDonnell Genome Institute Genome Technology Access Center, Washington University in St. Louis School of Medicine Genome Technology Access Center Core Facility, Washington University in St. Louis McDonnell Genome Institute Genome Technology Access Center, Washington University School of Medicine GTAC | 2026-08-15 11:21:51 | 6 | |||||
|
PNA Bio Resource Report Resource Website 1+ mentions |
PNA Bio (RRID:SCR_001037) | service resource, production service resource | A company which provides peptide nucleic acid products for use in research. It also provides engineered nuclease services to laboratories. | peptide nucleic acid, commercial, lab services, production service resource | is listed by: ScienceExchange | Available to the research community, Products are for research use only | SciEx_13409 | http://www.scienceexchange.com/facilities/pna-bio | SCR_001037 | PNA Bio Inc | 2026-08-15 11:21:51 | 2 | |||||||
|
flowWorkspace Resource Report Resource Website 1+ mentions |
flowWorkspace (RRID:SCR_001155) | software resource | Software package that facilitates comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis. | software package, mac os x, unix/linux, windows, r, data import, data representation, flow cytometry, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23020243 | Free, Available for download, Freely available | OMICS_05616 | SCR_001155 | flowWorkspace - Import flowJo Workspaces into BioConductor and replicate flowJo gating with flowCore | 2026-08-15 11:21:52 | 3 | |||||||
|
Renovo Neural Resource Report Resource Website 1+ mentions |
Renovo Neural (RRID:SCR_001035) | service resource, production service resource | A specialized preclinical research organization that provides services for biological research and development on neural therapies. Renovo offers preclinical assays and 3D-electron microscopy services that provide routine and customized solutions for basic science, preclinical and clinical research, and drug development. | commercial, solution, production service resource, preclinical, research, biological service | is listed by: ScienceExchange | THIS RESOURCE IS NO LONGER IN SERVICE | SciEx_12107 | SCR_001035 | Renovo Neural Inc, Renovo | 2026-08-15 11:21:50 | 1 | ||||||||
|
Insight Segmentation and Registration Toolkit Resource Report Resource Website 50+ mentions |
Insight Segmentation and Registration Toolkit (RRID:SCR_001149) | ITK | data or information resource, portal, topical portal, software resource | Open source, cross platform library that provides developers with extensive suite of software tools for image analysis. Developed through extreme programming methodologies, ITK builds on proven, spatially oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions. | registration, segmentation, multidimension, image processing, reusable library, analyze, bshort/bfloat, c++, console (text based), dicom, java, minc2, nifti, nrrd, os independent, philips par/rec, python, tcl/tk |
uses: Laplace Beltrami Filter on QuadEdge Meshes uses: VTK is used by: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI is used by: Displacement Field Viewer is used by: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Vaa3D is related to: elastix is related to: VMTK in 3D Slicer is related to: NA-MIC Kit is related to: SimpleITK |
NIBIB EB006733; NIBIB EB008374; NIBIB EB009634; NCRR P41RR013218 |
Free, Available for download, Freely available | nif-0000-00319 | http://www.nitrc.org/projects/insighttoolkit | SCR_001149 | Insight Toolkit, National Library of Medicine Insight Segmentation and Registration Toolkit (ITK), Insight Segmentation and Registration Toolkit | 2026-08-15 11:21:52 | 84 | |||||
|
GimmeMotifs Resource Report Resource Website 1+ mentions |
GimmeMotifs (RRID:SCR_001146) | GimmeMotifs | software resource | Software that provides a de novo motif prediction pipeline, especially suited for ChIP-seq datasets. It incorporates several existing motif prediction algorithms in an ensemble method to predict motifs and clusters these motifs using the WIC similarity scoring metric., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | linux, chip-seq, motif, cluster, python, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Radboud University; Nijmegen; The Netherlands |
PMID:21081511 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:gimmemotifs, OMICS_02150 | https://bio.tools/gimmemotifs | SCR_001146 | GimmeMotifs: a systematic de novo motif prediction pipeline | 2026-08-15 11:22:02 | 4 | |||||
|
Visualization and Analysis of Networks containing Experimental Data (VANTED) Resource Report Resource Website 10+ mentions |
Visualization and Analysis of Networks containing Experimental Data (VANTED) (RRID:SCR_001138) | VANTED | data processing software, software application, data analysis software, software resource, data visualization software | Software tool for extendable network visualization and analysis for the life sciences. It is Java-based and allows users to create, edit and map data onto existing or new networks. Experimental datasets can be visualized on network elements as graphical charts to show time series data or data of different treatments, as well as environmental conditions in the context of the underlying biological processes. Users can utilize built-in statistical algorithms to evaluate mapped data. | binary executable, simulation software, signal processing software, java, network visualization, statistical analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:23140568 | Open source | biotools:vanted, nif-0000-00373 | https://bitbucket.org/vanted-dev/vanted/src, https://bio.tools/vanted | http://vanted.ipk-gatersleben.de/ | SCR_001138 | Visualization and Analysis of Networks containing Experimental Data, VANTED v2 | 2026-08-15 11:21:52 | 14 | ||||
|
rbsurv Resource Report Resource Website 1+ mentions |
rbsurv (RRID:SCR_001175) | rbsurv | software resource | Software package that selects genes associated with survival. | microarray, gene, survival, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | biotools:rbsurv, BioTools:rbsurv, OMICS_02088 | https://bio.tools/rbsurv, https://bio.tools/rbsurv, https://bio.tools/rbsurv | SCR_001175 | rbsurv - Robust likelihood-based survival modeling with microarray data | 2026-08-15 11:22:03 | 1 | ||||||
|
CrossMap Resource Report Resource Website 10+ mentions |
CrossMap (RRID:SCR_001173) | CrossMap | software resource | A software program for convenient conversion of genome coordinates (or annotation files) between different assemblies. It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF. It is designed to liftover genome coordinates between assemblies. It?s not a program for aligning sequences to reference genome. CrossMap is not recommend for converting genome coordinates between species. | genome, assembly |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24351709 | GNU General Public License | OMICS_02184 | SCR_001173 | 2026-08-15 11:21:52 | 19 | |||||||
|
Sherman Resource Report Resource Website 100+ mentions |
Sherman (RRID:SCR_001294) | Sherman | software resource | Software tool to simulate FastQ files for high-throughput sequencing experiments. It allows the user to introduce various "contaminants" into the sequences, such as basecall errors, SNPs, adapter fragments etc., in order to evaluate the influence of common problems observed in many Next-Gen Sequencing experiments. | perl, bisulfite sequencing, high-throughput sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Babraham Institute |
Free, Available for download, Freely available | biotools:sherman, OMICS_02041 | http://www.bioinformatics.babraham.ac.uk/projects/sherman/ | SCR_001294 | Sherman - bisulfite-treated Read FastQ Simulator | 2026-08-15 11:21:55 | 124 | ||||||
|
STRViper Resource Report Resource Website 1+ mentions |
STRViper (RRID:SCR_001179) | STRViper | software resource | Software tool for detection of short tandem repeat (STR) variations from paired-end next generation sequencing data. It makes variant calls based on deviations in sequence fragment sizes, allowing the analysis of repeats of size up to fragment length. This stratergy also helps avoiding false calls resulting from errors arised from sequencing of repeat DNA. | next-generation sequencing, short tandem repeat variation, short tandem repeat, java, unix, linux, macos, paired-end read |
is listed by: OMICtools has parent organization: University of Queensland; Brisbane; Australia |
PMID:24353318 | Free, Available for download, Freely available | OMICS_02177 | SCR_001179 | Short Tandem Repeat Variation Indentification from Paired-End Reads, STRViper: Short Tandem Repeat Variation Indentification from Paired-End Reads | 2026-08-15 11:22:03 | 1 | ||||||
|
Golden Helix GenomeBrowse Resource Report Resource Website 1+ mentions |
Golden Helix GenomeBrowse (RRID:SCR_001213) | GenomeBrowse | commercial organization, data processing software, software application, software resource, data visualization software | Software tool that delivers visualizations of your genomic data that give you the power to see what is occurring at each base pair in your samples. A high performance backend is paired with an user interface to make sure that your discovery process is fluid and streamlined. | Golden Helix, variant, visualization, genome |
is listed by: OMICtools has parent organization: Golden Helix Incorporated |
Free, Available for download, Freely available | OMICS_02129 | SCR_001213 | 2026-08-15 11:21:53 | 2 | ||||||||
|
PARalyzer Resource Report Resource Website 1+ mentions |
PARalyzer (RRID:SCR_001208) | PARalyzer | software resource | Software tool to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. The algorithm utilizes the deep sequencing reads generated by the newly developed PAR-CLIP (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) protocol. The use of photoactivatable nucleotides in the PAR-CLIP protocol results in a more efficient crosslinking between the RNA-binding protein and its target relative to other CLIP methods; in addition a nucleotide substitution occurs at the site of crosslinking during Illumina library preparation. PARalyzer utilizes this nucleotide substition in a kernel density estimate classifier to generate the high resolution set of Protein-RNA interaction sites. | interaction, rna-binding protein, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Duke University; North Carolina; USA |
PMID:21851591 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:paralyzer, OMICS_02137 | https://bio.tools/paralyzer | SCR_001208 | PAR-CLIP data analyzer, PARalyzer (PAR-CLIP data analyzer) | 2026-08-15 11:21:53 | 7 | |||||
|
CGH-Explorer Resource Report Resource Website 10+ mentions |
CGH-Explorer (RRID:SCR_001283) | CGH-Explorer | software resource | Software program for visualization and statistical analysis of microarray-based comparative genomic hybridization (array-CGH) data. The program has preprocessing facilities, tools for graphical exploration of individual arrays or groups of arrays, and tools for statistical identification of regions of amplification and deletion. | microarray, comparative genomic hybridization, visualization, statistics, java, windows |
is listed by: OMICtools has parent organization: University of Oslo; Oslo; Norway |
PMID:15531610 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02054 | SCR_001283 | 2026-08-15 11:21:55 | 15 | |||||||
|
GeneMeta Resource Report Resource Website 1+ mentions |
GeneMeta (RRID:SCR_001201) | GeneMeta | data processing software, software application, data analysis software, software resource | Software package providing a collection of meta-analysis tools for analysing high throughput experimental data. | sequencing, high throughput |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02120 | SCR_001201 | GeneMeta - MetaAnalysis for High Throughput Experiments | 2026-08-15 11:21:53 | 1 | |||||||
|
methylMnM Resource Report Resource Website 1+ mentions |
methylMnM (RRID:SCR_001289) | methylMnM | software resource | Software package to detect different methylation levels (DMR) that gives the exact p-value and q-value of MeDIP-seq and MRE-seq data for different samples comparison. | dna methylation, sequencing, medip-seq, mre-seq |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v3 | OMICS_02047 | SCR_001289 | methylMnM - detect different methylation level (DMR) | 2026-08-15 11:22:04 | 9 | |||||||
|
Merck Resource Report Resource Website 10000+ mentions |
Merck (RRID:SCR_001287) | Merck | commercial organization | An American pharmaceutical company aiming to make a difference in the lives of people globally through their medicines, vaccines, biologic therapies and animal health products. | pharmaceutical, merck sharp & dohme corp, merck sharp and dohme corp, merck sharp and dohme, merck sharp & dohme corp., msd, medicine, endocrinology, neuroscience, oncology, respiratory, immunology, vaccine, animal health, veterinary |
uses: Kaggle uses: Tableau Desktop uses: FluoroFinder is affiliated with: European Federation of Pharmaceutical Industries and Associations is related to: eTRIKS is related to: OncoTrack is related to: European Lead Factory is related to: GetReal is related to: Investigator Databank is related to: Kinetics for Drug Discovery is related to: MIP-DILI is related to: ORBITO is related to: PharmaCog is related to: Asian Cancer Research Group is related to: Open PHACTS is related to: Collaboratory of AIDS Researchers for Eradciation (CARE) is parent organization of: MEDINA Foundation is parent organization of: Asian Cancer Research Group is parent organization of: Asia Training Consortium |
Diabetes, Cancer, Cardiovascular disease, Infectious disease | Crossref funder ID: 100004334, grid.417993.1, Wikidata: Q247489, ISNI: 0000 0001 2260 0793, nlx_152409 | https://ror.org/02891sr49 | SCR_001287 | Merck and Co., Merck and Co. Inc., Merck & Co. Inc., Merck & Co. | 2026-08-15 11:21:54 | 10286 | ||||||
|
ProbRNA Resource Report Resource Website 1+ mentions |
ProbRNA (RRID:SCR_001288) | ProbRNA | software resource | Software for computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data. | high-throughput sequencing, probe, rna structure, rna, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Chinese University of Hong Kong; Hong Kong; China |
PMID:24376038 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:probrna, OMICS_02195 | https://bio.tools/probrna | SCR_001288 | 2026-08-15 11:21:55 | 1 | ||||||
|
BlindCall Resource Report Resource Website 1+ mentions |
BlindCall (RRID:SCR_001280) | BlindCall | software resource | Software for ultra-fast base-calling of second-generation sequencing data by blind deconvolution. | base-calling, second-generation sequencing, blind deconvolution |
is listed by: OMICtools has parent organization: University of Maryland; Maryland; USA |
PMID:24413520 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02216 | SCR_001280 | 2026-08-15 11:22:04 | 1 | |||||||
|
VCFtools Resource Report Resource Website 1000+ mentions |
VCFtools (RRID:SCR_001235) | software application, software resource, data management software | Software package for working with VCF files. Used to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.Implements various utilities for processing Variant Call Format files, including validation, merging, comparing. Provides general Perl API. | perl, genetic variation, variant call format, software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:21653522 DOI:10.1093/bioinformatics/btr330 |
Free, Available for download, Freely available | OMICS_02105, biotools:vcftools, SCR_012092, OMICS_05112 | https://bio.tools/vcftools, https://sources.debian.org/src/vcftools/ | http://vcftools.sourceforge.net/ | SCR_001235 | Variant Call Format Tools | 2026-08-15 11:21:54 | 4555 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on RRID then you can log in from here to get additional features in RRID such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
