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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
NF Data Portal Resource Report Resource Website 1+ mentions |
NF Data Portal (RRID:SCR_021683) | portal, service resource, data or information resource, data repository, storage service resource | Portal created to help openly explore and share NF datasets, analysis tools, resources, and publications related to neurofibromatosis and schwannomatosis.Public data repository that stores and shares data generated by multiple collaborative research programs focused on neurofibromatosis diseases. | Sage Bionetworks, NF datasets, neurofibromatosis data, schwannomatosis data, neurofibromatosis diseases | uses: Synapse | neurofibromatosis type 1 (NF1), neurofibromatosis type 2 (NF2), and schwannomatosis (SCH) | Childrens Tumor Foundation ; Neurofibromatosis Therapeutic Acceleration Program |
PMID:31836719 | Free, Freely available | r3d100013571 | https://doi.org/10.17616/R31NJMYR | SCR_021683 | Neurofibromatosis Data Portal | 2026-08-12 10:52:42 | 5 | ||||
|
LMAS Resource Report Resource Website 1+ mentions |
LMAS (RRID:SCR_022251) | image reconstruction software, image analysis software, software application, data processing software, software resource | Automated workflow enabling benchmarking of traditional and metagenomic prokaryotic de novo assembly software using defined mock communities. Results are presented in interactive HTML report where selected global and reference specific performance metrics can be explored. | Shotgun metagenomics, genomic assembler | has parent organization: Ben-Gurion University of the Negev; Beer-Sheva; Israel | Free, Available for download, Freely available | SCR_022251 | Last (Meta)Genomic Assembler Standing | 2026-08-12 10:52:51 | 1 | |||||||||
|
SNP-sites Resource Report Resource Website 1+ mentions |
SNP-sites (RRID:SCR_022265) | data processing software, data analysis software, software resource, software application | Software tool to find SNP sites from multi-FASTA alignment file. Can output results in multiple formats for downstream analysis. | find SNP sites, Single Nucleotide Polymorphisms, single nucleotide polymorphisms extracting, large whole genome alignment, | Free, Available for download, Freely available | https://github.com/sanger-pathogens/snp-sites | SCR_022265 | Single Nucleotide Polymorphisms-sites | 2026-08-12 10:52:41 | 3 | |||||||||
|
purge dups Resource Report Resource Website 500+ mentions |
purge dups (RRID:SCR_021173) | data processing software, data analysis software, software resource, software application | 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. | haplotypic duplication identification, remove haplotigs overlap, remove contig overlaps, de novo assembly, read depth | Free, Available for download, Freely available | SCR_021173 | purge_dups | 2026-08-12 10:52:31 | 503 | ||||||||||
|
EZcalcium Resource Report Resource Website 1+ mentions |
EZcalcium (RRID:SCR_022354) | data processing software, data analysis software, software resource, software application | Software package for MATLAB that makes motion correction, segmentation, signal extraction and dimension reduction, analysis, and visualization of calcium imaging data easy to implement. Open source toolbox for analysis of calcium imaging data. | OpenBehavior, neural signal analysis, neural recording, optical imaging, analyze calcium imaging data |
is listed by: OpenBehavior has parent organization: David Geffen School of Medicine at UCLA; California; USA |
DOI:10.3389/fncir.2020.00025 | Free, Available for download, Freely available | https://github.com/porteralab/EZcalcium | SCR_022354 | 2026-08-12 10:52:30 | 3 | ||||||||
|
UMI4Cats Resource Report Resource Website 1+ mentions |
UMI4Cats (RRID:SCR_021780) | data visualization software, software application, data processing software, software resource, data analysis software | Software R package for analyzing UMI-4C chromatin contact data. Used to analyze chromatin contact profiles obtained by UMI-4C. | Profile and quantitatively compare, targeted chromosomal contact profiles, unique molecular identifiers, combines chromosome conformation capture | DOI:10.1093/bioinformatics/btab392 | Free, Available for download, Freely available | https://bioconductor.org/packages/UMI4Cats/, https://github.com/Pasquali-lab/UMI4Cats | SCR_021780 | Unique Molecular Identifiers combines chromosome conformation capture | 2026-08-12 10:52:44 | 2 | ||||||||
|
GuPPy Resource Report Resource Website 10+ mentions |
GuPPy (RRID:SCR_022353) | data processing software, data analysis software, software resource, software application | Software Python toolbox that makes fiber photometry data analysis intuitive and light on programming.Used to measure neural activity of freely behaving animals. | OpenBehavior, photometry analysis, neural activity measure, freely behaving animals |
is listed by: OpenBehavior has parent organization: Northwestern University Feinberg School of Medicine; Illinois; USA |
DOI:10.1038/s41598-021-03626-9 | https://github.com/LernerLab/GuPPy | SCR_022353 | Guided Photometry Analysis in Python | 2026-08-12 10:52:42 | 18 | ||||||||
|
Computational Analysis of gene Family Evolution Resource Report Resource Website 10+ mentions |
Computational Analysis of gene Family Evolution (RRID:SCR_018924) | CAFE | data processing software, data analysis software, software resource, software application | 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. | Computational analysis, gene family evolution, evolution statistical analysis, gene family size, gene evolution, phylogeny | has parent organization: Indiana University; Indiana; USA | NHGRI R33 HG003070; NSF MCB 0528465; METACyt Initiative of Indiana University ; Lilly Endowment ; Inc |
PMID:16543274 | SCR_018924 | CAFE v2.0, CAFE v4.0, CAFE v3.0, CAFE v5.0, Computational Analysis of gene Family Evolution | 2026-08-12 10:52:15 | 17 | |||||||
|
Simple Behavior Analysis Resource Report Resource Website 10+ mentions |
Simple Behavior Analysis (RRID:SCR_021413) | software toolkit, software application, data processing software, software resource, data analysis software | Open source software toolkit for computer classification of complex social behaviors in experimental animals. | Complex social behaviors classifications, supervised behavioral classifiers development, score behaviors across different background settings, OpenBehavior |
is listed by: OpenBehavior is related to: Simple Behavior Analysis project |
DOI:10.1101/2020.04.19.049452 | Free, Available for download, Freely Available | https://edspace.american.edu/openbehavior/project/simba/ | SCR_021413 | SimBA | 2026-08-12 10:52:19 | 16 | |||||||
|
Mouse Action Recognition System Resource Report Resource Website 1+ mentions |
Mouse Action Recognition System (RRID:SCR_022347) | MARS | data processing software, data analysis software, software resource, software application | Software Python pipeline for automated detection, pose estimation, and behavior classification in socially interacting mice.Used for pose estimation and behavior quantification in pairs of freely behaving mice. | OpenBehavior, behavior measurement, video analysis, real time recording and analysis, pose estimation and behavior quantification, freely behaving mice |
is listed by: OpenBehavior is related to: MARS Developer has parent organization: Northwestern University; Illinois; USA |
DOI:10.7554/eLife.63720 | Free, Available for download, Freely available | https://github.com/neuroethology/MARS | SCR_022347 | 2026-08-12 10:52:42 | 8 | |||||||
|
triku Resource Report Resource Website 1+ mentions |
triku (RRID:SCR_020977) | data processing software, data analysis software, software resource, software application | Software tool as feature selection method based on nearest neighbors for single-cell data. | Selection method, nearest neighbors, single cell data, data analysis | uses: scanpy | Free, Available for download, Freely available | https://triku.readthedocs.io/en/latest/ | SCR_020977 | 2026-08-12 10:52:15 | 2 | |||||||||
|
DrivAER Resource Report Resource Website 1+ mentions |
DrivAER (RRID:SCR_019076) | data processing software, data analysis software, software resource, software application | 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. | Manifold interpretation, scRNAseq data, relevance scores infering, transcriptional program, psuedotemporal ordering, disease status, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:drivaer | https://bio.tools/drivaer | SCR_019076 | Driving transcriptional programs using AutoEncoder based Relevance scores | 2026-08-12 10:52:12 | 1 | |||||||
|
AutoStereota Resource Report Resource Website 1+ mentions |
AutoStereota (RRID:SCR_022330) | data or information resource, instrument resource, project portal, portal | Automated surgical instrument for brain tissue aspiration.Instrument for microendoscope implantation. Utilizes robotic control of needle connected to vacuum pump to aspirate brain tissue. System consists of robotic surgical instrument built around commercially available stereotaxic instrument and open source MATLAB-based GUI for control. | OpenBehavior, Instrument, brain tissue aspiration, microendoscope implantation | is listed by: OpenBehavior | DOI:10.1016/j.jneumeth.2018.10.013 | Free, Freely available | https://github.com/liang-bo/AutoStereota | SCR_022330 | 2026-08-12 10:52:52 | 3 | ||||||||
|
STENCIL Resource Report Resource Website 1+ mentions |
STENCIL (RRID:SCR_021878) | data processing software, data visualization software, software resource, software application | Web engine for visualizing and sharing life science datasets.Designed to organize, visualize, and enable sharing of interactive genomic data visualizations. Provides ability to inspect and interpret sequencing data, without requiring programming expertise. | Visualizing genomic data, sharing genomic data, interactive genomic data visualizations, interpret sequencing data | NIEHS ES013768; NIGMS GM125722 |
DOI:10.1101/2021.06.04.447108 | Free, Available for download, Freely available | SCR_021878 | 2026-08-12 10:52:38 | 4 | |||||||||
|
Genomic Association Tester Resource Report Resource Website 10+ mentions |
Genomic Association Tester (RRID:SCR_020949) | GAT | simulation software, software application, data processing software, software resource, data analysis software | Software tool as simulation framework for testing association of genomic intervals. Used for estimating significance of overlap between multiple sets of genomic intervals. Estimates statistical significance based on simulation and controls for multiple tests using false discovery rate. | Genomic intervals, genomic intervals association testing, overlap significance estimation, genomic intervals sets, segment length distribution, chromosomal location, isochores | UK Medical Research Council | PMID:23782611 | Free, Available for download, Freely available | https://github.com/AndreasHeger/gat | http://code.google.com/p/genomic-association-tester | SCR_020949 | 2026-08-12 10:52:27 | 31 | ||||||
|
PM4NGS Resource Report Resource Website 1+ mentions |
PM4NGS (RRID:SCR_019164) | data management software, software toolkit, software application, data processing software, software resource, data analysis software, workflow software | Software tool to generate standard organizational structure for Next Generation Sequencing data analysis. Includes directory structure for project, several Jupyter notebooks for data management and CWL workflows for pipeline execution. | NGS workflow, standard organizational structure generation, Next Generation Sequencing data, NGS data analysis, NGS data analysis workflow, data integration, Jupyter notebook, CWL format, bio.tools |
is listed by: bio.tools is listed by: Debian |
Intramural Research Program of the National Library of Medicine NIH | DOI:10.7490/f1000research.1117155.1 | Free, Freely available | biotools:pm4ngs | https://bio.tools/pm4ngs | SCR_019164 | Project Manager for Next Generation Sequencing | 2026-08-12 10:52:12 | 1 | |||||
|
Panaroo Resource Report Resource Website 10+ mentions |
Panaroo (RRID:SCR_021090) | data processing software, data analysis software, software resource, software application | 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. | pangenome investigation, correct errors, genomes, large structural variants, bacterial genomes | Free, Available for download, Freely available | https://gtonkinhill.github.io/panaroo/#/gettingstarted/quickstart | SCR_021090 | Bacterial Pangenome Analysis Pipeline | 2026-08-12 10:52:16 | 32 | |||||||||
|
Tandem Repeats Finder Resource Report Resource Website 100+ mentions |
Tandem Repeats Finder (RRID:SCR_022065) | sequence analysis software, software application, data processing software, software resource, data analysis software | Software tool to locate and display tandem repeats in DNA sequences. Used to analyze DNA sequences. | locate and display tandem repeats, analyze DNA sequences, tandem repeat, DNA sequence | PMID:9862982 | Free, Available for download, Freely available | SCR_022065 | 2026-08-12 10:52:40 | 443 | ||||||||||
|
Brain Cell Methylation Viewer Resource Report Resource Website 1+ mentions |
Brain Cell Methylation Viewer (RRID:SCR_020954) | mC Viewer | service resource, data or information resource, production service resource, data access protocol, software resource, analysis service resource, web service | Viewer for DNA Methylation Atlas of Mouse Brain at Single Cell Resolution. Browser to interactively explore single cell methylome dataset including exploration of methylation diversity of one gene at single-cell or cell-type level, exploration of cell type composition of adult mouse brain dissection regions and anatomical structures, explorartion of spatial distribution and methylation signature genes of one cell type. | BRAIN Initiative Cell Census Network, mouse brain, cell types, epigenomes, single cell exploration, methylome dataset | has parent organization: Salk Institute for Biological Studies | DOI:10.1101/2020.04.30.069377 | Free, Freely available | SCR_020954 | Neomorph: Brain Cell Methylation Viewer | 2026-08-12 10:52:15 | 2 | |||||||
|
CSpritz Resource Report Resource Website 1+ mentions |
CSpritz (RRID:SCR_021884) | software resource, data access protocol, web service | Web tool for prediction of intrinsic protein disorder segments with annotation for homology, secondary structure and linear motifs. | Intrinsic protein disorder segments prediction, homology, secondary structure, linear motifs, annotation | University of Padova ; Italian Ministry of Education |
DOI:10.1093/nar/gkr411 | Free, Freely available | SCR_021884 | 2026-08-12 10:52:38 | 2 |
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.
