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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Human Reference Protein Interactome Project Resource Report Resource Website 10+ mentions |
Human Reference Protein Interactome Project (RRID:SCR_015670) | HuRI | portal, database, web application, data or information resource, software resource, project portal | Project portal for the Human Reference Protein Interactome Project, which aims generate a first reference map of the human protein-protein interactome network by identifying binary protein-protein interactions (PPIs). It achieves this by systematically interrogating all pairwise combinations of predicted human protein-coding genes using proteome-scale technologies. | protein interactome, protein-protein interaction, ppi, pairwise combination, proteome, human reference | NHGRI R01/U01HG001715; NHGRI P50HG004233; NHLBI U01HL098166; NHLBI U01HL108630; NCI U54CA112962; NCI R33CA132073; NIH RC4HG006066; NICHD ARRA R01HD065288; NICHD ARRA R21MH104766; NICHD ARRA R01MH105524; NIMH R01MH091350; NSF CCF-1219007; NSERC RGPIN-2014-03892 |
PMID:25416956 | Freely Available, Free, Available for download | SCR_015670 | HuRI: The Human Reference Protein Interactome Mapping Project | 2026-08-03 09:36:22 | 20 | |||||||
|
Seurat Resource Report Resource Website 5000+ mentions |
Seurat (RRID:SCR_016341) | software toolkit, software application, data processing software, data analysis software, software resource | 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. | single, cell, genomic, RNA-seq, data, QC, analysis, source, heterogeneity, transcriptomic, measurement, integrate, diverse |
is used by: Stardust is used by: Seurat MapQuery is related to: DoubletFinder is related to: Azimuth works with: SeuratWrappers works with: Connectome |
NHGRI 1DP2HG009623; NIMH 5R01MH071679; NSF |
PMID:29608179 | Free, Available for download, Freely available | https://satijalab.org/seurat/get_started.html | SCR_016341 | 2026-08-03 09:36:43 | 9395 | |||||||
|
LeafCutter Resource Report Resource Website 10+ mentions |
LeafCutter (RRID:SCR_017639) | software application, data processing software, data analysis software, data analytics software, software resource | Software tool for identifying and quantifying RNA splicing variation. Used to study sample and population variation in intron splicing. Identifies variable intron splicing events from short read RNA-seq data and finds alternative splicing events of high complexity. Used for detecting differential splicing between sample groups, and for mapping splicing quantitative trait loci (sQTLs). | Identify, quantitate, RNA, splicing, variation, intron, short, read, RNAseq, data, mapping, trait, loci, sQTL | has parent organization: Stanford University; Stanford; California | CEHG Fellowship ; Howard Hughes Medical Institute ; NHGRI HG007036; NHGRI HG008140; NHGRI HG009431; NIMH R01 MH107666 |
PMID:29229983 DOI:10.1038/s41588-017-0004-9 |
Free, Available for download, Freely available | SCR_017639 | 2026-08-03 09:36:53 | 29 | ||||||||
|
Computational Analysis of gene Family Evolution Resource Report Resource Website 10+ mentions |
Computational Analysis of gene Family Evolution (RRID:SCR_018924) | CAFE | software resource, data processing software, software application, data analysis software | 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 | 2026-08-03 09:37:21 | 16 | |||||||
|
Drop-seq tools Resource Report Resource Website 50+ mentions |
Drop-seq tools (RRID:SCR_018142) | software resource, data processing software, software application, data analysis software | 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. | Simultaneous analysis, Drop-seq data, gene expression, thousands individual cells |
is listed by: Debian has parent organization: Broad Institute |
Stanley Center for Psychiatric Research ; MGH Psychiatry Residency Research Program ; Stanley-MGH Fellowship in Psychiatric Neuroscience ; Stewart Trust Fellows Award ; Simons Foundation ; NHGRI P50 HG006193; Klarman Cell Observatory ; NIMH U01 MH105960; NIMH R25 MH094612; NICHD F32 HD075541; NSF ECS 0335765; NSF DMR 1310266; NSF DMR 1420570 |
PMID:26000488 | https://sources.debian.org/src/drop-seq-tools/ | SCR_018142 | Droplet sequencing tools, Droplet sequencing data analysis software tools | 2026-08-03 09:36:59 | 94 | |||||||
|
Shannon Resource Report Resource Website 1+ mentions |
Shannon (RRID:SCR_017037) | software resource, data processing software, software application, data analysis software | Software tool for de novo transcriptome assembly from RNA-Seq data. | de novo, transcriptome, assembly, RNAseq, data |
has parent organization: University of Washington; Seattle; USA has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Stanford University; Stanford; California |
NSF Center for Science of Information ; NHGRI ; University of Washington |
Free, Available for download, Freely available | http://sreeramkannan.github.io/Shannon/ | SCR_017037 | 2026-08-03 09:36:59 | 1 | ||||||||
|
SNPRelate Resource Report Resource Website 10+ mentions |
SNPRelate (RRID:SCR_022719) | software resource, data processing software, software application, data analysis software | Software R package as parallel computing toolset for relatedness and principal component analysis of SNP data. | parallel computing, relatedness and principal component analysis, SNP data analysis | NHGRI U01 HG 004446 | PMID:23060615 | Free, Available for download, Freely available | https://github.com/zhengxwen/SNPRelate | SCR_022719 | 2026-08-03 09:37:47 | 12 | ||||||||
|
hifiasm-meta Resource Report Resource Website 1+ mentions |
hifiasm-meta (RRID:SCR_022771) | software resource, data processing software, software application, data analysis software | Software tool as metagenome assembler that exploits high accuracy of recent data. De novo metagenome assembler, based on haplotype resolved de novo assembler for PacBio Hifi reads. Workflow consists of optional read selection, sequencing error correction, read overlapping, string graph construction and graph cleaning. | Error correction, read overlapping, hifiasm, haplotype resolved de novo assembler, PacBio Hifi reads | NHGRI R01HG010040; NHGRI U01HG010971 |
PMID:35534630 | Free, Available for download, Freely available | SCR_022771 | hifiasm_meta | 2026-08-03 09:37:48 | 2 | ||||||||
|
ComplexUpset Resource Report Resource Website 10+ mentions |
ComplexUpset (RRID:SCR_022752) | software resource, data processing software, software application, data analysis software | Software R package for visualization of intersecting sets. Used for quantitative analysis of sets, their intersections, and aggregates of intersections. Visualizes set intersections in matrix layout and introduces aggregates based on groupings and queries. | visualization of intersecting sets, set intSections in matrix layout, aggregates based on groupings and queries, quantitative analysis of sets |
uses: ggplot2 is listed by: CRAN |
Austrian Science Fund ; Air Force Research Laboratory and DARPA ; NHGRI K99 HG007583 |
PMID:26356912 | Free, Available for download, Freely available | SCR_022752 | 2026-08-03 09:37:47 | 18 | ||||||||
|
sei Resource Report Resource Website 1+ mentions |
sei (RRID:SCR_022571) | web service, data access protocol, software resource | Web server for systematically predicting sequence regulatory activities and applying sequence information to human genetics data. Provides global map from any sequence to regulatory activities, as represented by sequence classes, and each sequence class integrates predictions for chromatin profiles like transcription factor, histone marks, and chromatin accessibility profiles across wide range of cell types. | systematically predicting sequence regulatory activities, applying sequence information, human genetics data, sequence class predictions | National Science Foundation Graduate Research Fellowship Program ; NHGRI R01HG005998; NHLBI U54HL117798; NIGMS R01GM071966 |
PMID:35817977 | Free, Available for download, Freely available | https://hb.flatironinstitute.org/sei | SCR_022571 | 2026-08-03 09:38:02 | 6 | ||||||||
|
UpSet Resource Report Resource Website 10+ mentions |
UpSet (RRID:SCR_022731) | software application, data processing software, data analysis software, software resource, data visualization software | Software tool to visualize set intersections in matrix layout. Interactive, web based visualization technique designed to analyze set based data. Visualizes both, set intersections and their properties, and elements in dataset. Used for quantitative analysis of data with more than three sets. | visualize set intersections, matrix layout, intersecting sets, more than three sets quantitative data analysis | Austrian Science Fund ; Air Force Research Laboratory ; DARPA ; NHGRI K99 HG007583 |
PMID:26356912 | Free, Available for download, Freely available | https://github.com/VCG/upset | SCR_022731 | UpSet Plot | 2026-08-03 09:37:47 | 16 | |||||||
|
SvABA Resource Report Resource Website 10+ mentions |
SvABA (RRID:SCR_022998) | sequence analysis software, software application, data processing software, data analysis software, software resource | Software tool for detecting structural variants in sequencing data using genome wide local assembly. Genome wide detection of structural variants and indels by local assembly. Used for detecting SVs from short read sequencing data using genome wide local assembly with low memory and computing requirements. | genome wide detection, structural variants, indels, local assembly | NHGRI T32 HG002295; NCI U54CA143798; NCI R01CA188228; DFCI-Novartis Drug Discovery Program ; Voices Against Brain Cancer ; Pediatric Low-Grade Astrocytoma Foundation ; Broad Institute ; Wellcome Fund Career Award for Medical Scientists |
PMID:29535149 | Free, Available for download, Freely available | SCR_022998 | 2026-08-03 09:37:52 | 14 | |||||||||
|
UpSetPlot Resource Report Resource Website 1+ mentions |
UpSetPlot (RRID:SCR_023225) | software resource, data visualization software, software application, data processing software | Software Python implementation of UpSet plots to visualize set overlaps. | UpSet plots, Python, visualize set overlaps, | Austrian Science Fund ; Air Force Research Laboratory ; DARPA ; NHGRI K99 HG007583 |
PMID:26356912 | Free, Available for download, Freely available | SCR_023225 | 2026-08-03 09:38:17 | 6 | |||||||||
|
CRISPOR Resource Report Resource Website 1000+ mentions |
CRISPOR (RRID:SCR_015935) | software resource, web application | Web application that helps design, evaluate and clone guide sequences for the CRISPR/Cas9 system. This sgRNA design tool assists with guide selection in a variety of genomes and pre-calculated results for all human coding exons as a UCSC Genome Browser track. | rna, sg, sgrna, crispr, genome, off-target, prediction, accuracy, clone, cas9, coding, exon | is related to: UCSC Genome Browser | MRC 53658; NIH Office of the Director U42 OD011174; NHGRI U41 HG002371; NCI U54 HG007990; California Institute of Regenerative Medicine GC1R-06673C; Agence Nationale pour la Recherche ; Fondation pour la Recherche Médicale DEQ20140329544 |
PMID:27380939 | Free, Available for download | https://github.com/maximilianh/crisporWebsite | SCR_015935 | 2026-08-03 09:36:30 | 1320 | |||||||
|
UCSC Cell Browser Resource Report Resource Website 100+ mentions |
UCSC Cell Browser (RRID:SCR_023293) | web service, data access protocol, software resource | Web based tool to visualize gene expression and metadata annotation distribution throughout single cell dataset or multiple datasets. Interactive viewer for single cell expression. You can click on and hover over cells to get meta information, search for genes to color on and click clusters to show cluster specific marker genes. | visualize gene expression, metadata annotation distribution, single cell data viewer, cluster specific marker genes, single cell expression, |
is related to: Allen Institute for Brain Science is related to: BRAIN Initiative Cell Atlas Network has parent organization: University of California at Santa Cruz; California; USA |
NHGRI 5U41HG002371; NHGRI 1U41HG010972; NHGRI 5R01HG010329; NIMH U01MH114825; NINDS K99 NS111731; NIMH RF1MH121268; NIMH DP2MH122400; Silicon Valley Community Foundation ; California Institute for Regenerative Medicine ; University of California Office of the President Emergency COVID-19 Research Seed Funding ; Chan Zuckerberg Initiative Foundation ; Simons Foundation ; Brain and Behavior Research Foundation |
PMID:34244710 | Free, Freely available | https://cellbrowser.readthedocs.io/en/master/, https://github.com/maximilianh/cellBrowser | SCR_023293 | 2026-08-03 09:38:09 | 123 | |||||||
|
HetMatPy Resource Report Resource Website 1+ mentions |
HetMatPy (RRID:SCR_023409) | network analysis software, software application, data processing software, data analysis software, software resource | Software Python package for matrix storage and operations on hetnets. Enables identifying relevant network connections between set of query nodes. | Hetionet, matrix storage, operations on hetnets, hetnets, heterogeneous networks, | Gordon and Betty Moore Foundation ; NHGRI R01 HG010067; NCI R01 CA237170 |
PMID:36711546 | Free, Available for download, Freely available | SCR_023409 | hetmatpy | 2026-08-03 09:38:10 | 1 | ||||||||
|
Alfred Resource Report Resource Website 10+ mentions |
Alfred (RRID:SCR_023354) | algorithm resource, software resource, web application | Web application as interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencingas. | alignment, BAM, quality control, cell barcode splitting, annotation directed improvement, BAM alignment statistics, feature counting, feature annotation. | NHGRI U41HG007497 | PMID:30520945 | Free, Available for download, Freely available | https://bio.tools/alfred | SCR_023354 | 2026-08-03 09:38:21 | 15 | ||||||||
|
PathVisio Resource Report Resource Website 10+ mentions |
PathVisio (RRID:SCR_023789) | software toolkit, software application, data processing software, software resource, data visualization software | Software visualization tool for biological pathways. Pathway analysis and drawing software which allows drawing, editing, and analyzing biological pathways. Developed in Java and can be extended with plugins. | biological pathway editor, pathway editor, visualization and analysis, extendable pathway analysis, | NIGMS R01 GM100039; Netherlands Consortium for Systems Biology ; NIGMS GM080223; NHGRI HG003053; Transnational University Limburg |
PMID:25706687 PMID:18817533 |
Free, Available for download, Freely available | SCR_023789 | PathVisio 3 | 2026-08-03 09:38:08 | 24 | ||||||||
|
Minimap2 Resource Report Resource Website 1000+ mentions |
Minimap2 (RRID:SCR_018550) | alignment software, software application, data processing software, image analysis software, software resource | Software tool as pairwise alignment for nucleotide sequences. Alignment program to map DNA or long mRNA sequences against large reference database. Versatile pairwise aligner for genomic and spliced nucleotide sequences. | Pairwise alignment, nucleotide sequence, map DNA sequence, map mRNA sequence, reference database, spliced nucleotide sequence, bio.tools, FASEB list |
is used by: D-GENIES is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01 HG010040 | PMID:29750242 | Free, Available for download, Freely available | OMICS_31658, biotools:minimap2 | https://bio.tools/minimap2, https://sources.debian.org/src/libminimap2-dev/ | SCR_018550 | 2026-08-03 09:36:59 | 1325 | ||||||
|
Monocle3 Resource Report Resource Website 100+ mentions |
Monocle3 (RRID:SCR_018685) | software toolkit, software application, data processing software, data analysis software, software resource | Software analysis toolkit for single cell RNA-seq. Used for single cell RNA-Seq experiments. Unsupervised algorithm that increases temporal resolution of transcriptome dynamics using single-cell RNA-Seq data collected at multiple time points. | Data analysis, singel cell RNAseq data, single cell RNAseq experiment, transcriptome dynamics | has parent organization: University of Washington; Seattle; USA | NIH Office of the Director DP2 OD00667; NIGMS P01 GM099117; NIH Office of the Director DP2 0D008514; NHGRI P50 HG006193; Single Cell Genomics initiative |
PMID:24658644 | Free, Available for download, Freely available | https://github.com/cole-trapnell-lab/monocle3 | SCR_018685 | Monocle, Monocle 3 | 2026-08-03 09:37:04 | 270 |
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.
