Searching the RRID Resource Information Network
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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
sei Resource Report Resource Website 1+ mentions |
sei (RRID:SCR_022571) | data access protocol, software resource, web service | 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 | 2026-02-16 09:50:25 | 6 | ||||||||
|
UpSet Resource Report Resource Website 10+ mentions |
UpSet (RRID:SCR_022731) | software application, data processing software, data visualization software, data analysis software, software resource | 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 | 2026-02-16 09:50:23 | 16 | |||||||
|
HetMatPy Resource Report Resource Website 1+ mentions |
HetMatPy (RRID:SCR_023409) | software application, data processing software, network analysis 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 | 2026-02-16 09:50:35 | 1 | ||||||||
|
UpSetPlot Resource Report Resource Website 1+ mentions |
UpSetPlot (RRID:SCR_023225) | software application, data processing software, data visualization software, software resource | 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 | 2026-02-16 09:50:36 | 6 | |||||||||
|
UCSC Cell Browser Resource Report Resource Website 100+ mentions |
UCSC Cell Browser (RRID:SCR_023293) | data access protocol, software resource, web service | 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 | 2026-02-16 09:50:28 | 123 | |||||||
|
PathVisio Resource Report Resource Website 10+ mentions |
PathVisio (RRID:SCR_023789) | software application, data processing software, software toolkit, data visualization software, software resource | 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 | 2026-02-16 09:50:41 | 24 | ||||||||
|
Genetic and Rare Diseases Information Center Resource Report Resource Website 10+ mentions |
Genetic and Rare Diseases Information Center (RRID:SCR_008695) | GARD | data or information resource, topical portal, disease-related portal, portal | Genetic and Rare Diseases Information Center (GARD) is a collaborative effort of two agencies of the National Institutes of Health, The Office of Rare Diseases Research (ORDR) and the National Human Genome Research Institute (NHGRI) to help people find useful information about genetic conditions and rare diseases. GARD provides timely access to experienced information specialists who can furnish current and accurate information about genetic and rare diseases. So far, GARD has responded to 27,635 inquiries on about 7,147 rare and genetic diseases. Requests come not only from patients and their families, but also from physicians, nurses and other health-care professionals. GARD also has proved useful to genetic counselors, occupational and physical therapists, social workers, and teachers who work with people with a genetic or rare disease. Even scientists who are studying a genetic or rare disease and who need information for their research have contacted GARD, as have people who are taking part in a clinical study. Community leaders looking to help people find resources for those with genetic or rare diseases and advocacy groups who want up-to-date disease information for their members have contacted GARD. And members of the media who are writing stories about genetic or rare diseases have found the information GARD has on hand useful, accurate and complete. GARD has information on: :- What is known about a genetic or rare disease. :- What research studies are being conducted. :- What genetic testing and genetic services are available. :- Which advocacy groups to contact for a specific genetic or rare disease. :- What has been written recently about a genetic or rare disease in medical journals. GARD information specialists get their information from: :- NIH resources. :- Medical textbooks. :- Journal articles. :- Web sites. :- Advocacy groups, and their literature and services. :- Medical databases. | genetic, disease, information, genome, human, rare disease, health, physician, counselor, gene, journal, medical | has parent organization: National Institutes of Health | Office of Rare Diseases Research ; NHGRI |
nif-0000-37627 | SCR_008695 | Genetic Rare Diseases Information Center | 2026-02-16 09:47:15 | 14 | |||||||
|
Pavian Resource Report Resource Website 10+ mentions |
Pavian (RRID:SCR_016679) | data analysis service, analysis service resource, web application, software resource, production service resource, service resource | Software R package for interactive analysis of metagenomics classification results with a special focus on infectious disease diagnosis. Used for analyzing and visualization of metagenomics classification results from classifiers such as Kraken, Centrifuge and MetaPhlAn. Provides an alignment viewer for validation of matches to a particular genome. | interactive, analysis, metagenomics, classification, result, infectious, disease, diagnosis, data, visualization, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Centrifuge Classifier |
NHGRI R01 HG006677; NIGMS R01 GM083873; U. S. Army Research Office W911NF1410490 |
DOI:10.1101/084715 | Free, Freely available | biotools:pavian | https://fbreitwieser.shinyapps.io/pavian/ https://bio.tools/pavian |
SCR_016679 | 2026-02-16 09:49:05 | 22 | ||||||
|
CheckMyMetal Resource Report Resource Website 1+ mentions |
CheckMyMetal (RRID:SCR_016887) | CMM | data access protocol, software resource, web service | Metal binding site validation server. Used for systematic inspection of the metal-binding architectures in macromolecular structures. The validation parameters that CMM examines cover the entire binding environment of the metal ion, including the position, charge and type of atoms and residues surrounding the metal. | metal, binging, site, validation, server, systematic, inspection, macromolecular, structure, ion, charge, position, atom | NIGMS GM117325; NHGRI HG008424; NIAID HHSN272201200026C |
PMID:28291757 | Free, Freely available | SCR_016887 | 2026-02-16 09:49:07 | 5 | ||||||||
|
PICRUSt Resource Report Resource Website 10+ mentions |
PICRUSt (RRID:SCR_016855) | PICRUSt | software application, software resource, simulation software | Software package to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Used to predict which gene families are present and then combines gene families to estimate the composite metagenome. | predict, metagenome, functional, content, DNA, sample, marker, gene, sequence, data, microbiome, 16S, RNA | is related to: PICRUSt2 | Canadian Institutes of Health Research ; Canada Research Chairs program ; Howard Hughes Medical Institute ; NIDDK P01 DK078669; NHGRI U01 HG004866; NHGRI R01 HG004872; Crohn’s and Colitis Foundation of America ; Sloan Foundation ; NHGRI R01 HG005969; NSF CAREER DBI1053486; ARO W911NF1110473 |
PMID:23975157 | Free, Available for download, Freely available | SCR_016856 | SCR_016855 | Phylogenetic Investigation of Communities by Reconstruction of Unobserved States, PICRUSt | 2026-02-16 09:49:06 | 36 | |||||
|
WTDBG Resource Report Resource Website 50+ mentions |
WTDBG (RRID:SCR_017225) | software application, data processing software, sequence analysis software, data analysis software, image analysis software, software resource, alignment software | Software tool as de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies. It assembles raw reads without error correction and then builds consensus from intermediate assembly output. Desiged to assemble huge genomes in very limited time. | sequence, assembler, de novo, long, noisy, read, likelihood, estimator, genome |
is listed by: OMICtools is listed by: Debian |
NSFC ; NHGRI R01 HG010040 |
PMID:31819265 | Free, Available for download, Freely available | OMICS_24025 | https://github.com/ruanjue/wtdbg https://sources.debian.org/src/wtdbg2/ |
SCR_017225 | Wtdbg2, wtdgb, Wtdgb, wtdgb2 | 2026-02-16 09:49:11 | 57 | |||||
|
Ngmlr Resource Report Resource Website 10+ mentions |
Ngmlr (RRID:SCR_017620) | NGMLR | software application, data processing software, image analysis software, software resource, alignment software | Software tool as long read mapper designed to align PacBio or Oxford Nanopore reads to reference genome and optimized for structural variation detection. | Long, read, mapper, align, PacBio, Oxford Nanopore, read, reference, genome, structural, variantion, detection, bio.tools |
is listed by: bio.tools is listed by: Debian |
National Science Foundation ; NHGRI R01 HG006677; NHGRI UM1 HG008898 |
PMID:29713083 | Free, Available for download, Freely available | biotools:ngmlr | https://bio.tools/ngmlr | SCR_017620 | coNvex Gap-cost alignMent for Long Reads | 2026-02-16 09:49:16 | 31 | ||||
|
NanoSim Resource Report Resource Website 10+ mentions |
NanoSim (RRID:SCR_018243) | software application, software resource, simulation software | Software tool as Nanopore sequence read simulator based on statistical characterization. Oxford Nanopore Technology sequence simulator written in Python and R. Benefits development of scalable next generation sequencing technologies for long nanopore reads, including genome assembly, mutation detection, and metagenomic analysis software. | Nanopore sequence read, sequence simulator, Oxford Nanopore Technology, next generation sequencing, long nanopore read, genome assembly, mutation detection, bio.tools, bio.tools |
is listed by: Debian is listed by: bio.tools |
NHGRI R01 HG007182; Genome Canada ; Genome British Columbia ; British Columbia Cancer Foundation ; University of British Columbia |
DOI:10.1093/gigascience/gix010 | Free, Available for download, Freely available | biotools:trans-nanosim, biotools:nanosim | https://www.bcgsc.ca/resources/software/nanosim https://bio.tools/nanosim https://bio.tools/Trans-NanoSim |
SCR_018243 | 2026-02-16 09:49:27 | 18 | ||||||
|
Minimap2 Resource Report Resource Website 1000+ mentions |
Minimap2 (RRID:SCR_018550) | software application, data processing software, image analysis software, software resource, alignment software | 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 | 2026-02-16 09:49:31 | 1325 | ||||||
|
Monocle3 Resource Report Resource Website 100+ mentions |
Monocle3 (RRID:SCR_018685) | software application, data processing software, software toolkit, 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 | 2026-02-16 09:49:31 | 270 | ||||||
|
QoRTs Resource Report Resource Website 10+ mentions |
QoRTs (RRID:SCR_018665) | software application, data processing software, software toolkit, data analysis software, software resource | Software package for quality control and data processing of RNA-Seq experiments. Software portable multifunction toolkit for assisting in analysis, quality control, and data management of RNA-Seq and DNA-Seq datasets. Used for detection and identification of errors, biases, and artifacts produced by high throughput sequencing technology. Can be used in operating system that supports Java and R. | Quality control, data processing, RNAseq data, DNAseq data, analysis, data management, error detection, biases, artifacts, high throughput sequencing technology, | NHGRI | PMID:26187896 | Free, Freely available | https://github.com/hartleys/QoRTs | SCR_018665 | 2026-02-16 09:49:32 | 26 | ||||||||
|
MyGene.info Resource Report Resource Website 10+ mentions |
MyGene.info (RRID:SCR_018660) | service resource, data access protocol, software resource, web service | Web service for querying or retrieving gene annotation data. | Querying gene, gene, annotation, gene annotation, annotation data, gene annotation data, retrieving gene annotation data, bio.tools |
is listed by: Debian is listed by: bio.tools |
NHGRI U01 HG008473; NIGMS GM083924; NIGMS U54 GM114833; NHGRI U01 HG006476; NCI K22 CA188163; NCATS UL1 TR001114; Scripps Translational Science Institute |
DOI:10.1186/s13059-016-0953-9 | Free, Freely available | biotools:mygene.info, BioTools:mygene.info | https://bio.tools/mygene.info https://bio.tools/mygene.info https://bio.tools/mygene.info |
SCR_018660 | 2026-02-16 09:49:30 | 20 | ||||||
|
GOnet Resource Report Resource Website 1+ mentions |
GOnet (RRID:SCR_018977) | web service, data access protocol, analysis service resource, software resource, production service resource, service resource | Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists. | Gene Ontology, interactive analysis, data, gene, protein, gene list, protein list, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools works with: Gene Ontology |
NIH Common Fund ; NIGMS ; NHGRI R24 HG010032; NIAID U19 AI118610; NIAID U19 AI118626 |
PMID:30526489 | biotools:GOnet | https://github.com/mikpom/gonet https://bio.tools/GOnet |
SCR_018977 | 2026-02-16 09:49:37 | 3 | |||||||
|
Biofactoid Resource Report Resource Website 1+ mentions |
Biofactoid (RRID:SCR_021011) | web service, portal, data access protocol, project portal, software resource, knowledge environment resource, data or information resource | Web tool for creating digital profile of scientific discoveries in article and connecting them to related research. Authors describe molecular interactions supported by their results, letting researchers explore first hand account of article findings and connect to related articles and knowledge. Web based system for scientists to compose structured representation of networks of interactions between genes, their products, and chemical compounds, represented using power of formal ontology. | Knowledge management, molecular interactions, pathway, compose network structured representation, digital profile, connect related articles, formal ontology |
is related to: Biological Pathways Exchange is related to: Biological Pathways Exchange has parent organization: University of Toronto; Ontario; Canada has parent organization: Harvard University; Cambridge; United States has parent organization: University of Oregon; Oregon; USA |
NHGRI U41HG006623; DARPA Big Mechanism |
Free, Freely available | SCR_021011 | 2026-02-16 09:49:56 | 1 | |||||||||
|
Hifiasm Resource Report Resource Website 500+ mentions |
Hifiasm (RRID:SCR_021069) | software application, data processing software, sequence analysis software, data analysis software, software resource | Software tool as haplotype resolved de novo assembler for PacBio Hifi reads. Can assemble human genome in several hours.Introduces new graph binning algorithm and achieves haplotype resolved assembly given trio data. Takes advantage of long high fidelity sequence reads to represent haplotype information in phased assembly graph. Preserves contiguity of all haplotypes. | PacBio Hifi reads, haplotype resolved de novo assembler, trio data, long high fidelity sequence reads, | NHGRI R01 HG010040; NHGRI U01 HG010961; NHGRI U41HG010972 |
PMID:33526886 | Free, Available for download, Freely available | SCR_021069 | 2026-02-16 09:49:56 | 544 |
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