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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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LINCS Information Framework Resource Report Resource Website 1+ mentions |
LINCS Information Framework (RRID:SCR_003937) | data or information resource, database | LIFE search engine contains data generated from LINCS Pilot Phase, to integrate LINCS content leveraging semantic knowledge model and common LINCS metadata standards. LIFE makes LINCS content discoverable and includes aggregate results linked to Harvard Medical School and Broad Institute and other LINCS centers, who provide more information including experimental conditions and raw data. Please visit LINCS Data Portal. | bioassay, cell, small molecule, kinase protein, compound, cell, gene, metadata standard, cell line, primary cell, rnai reagent, rnai, reagent, protein reagent, protein, antibody reagent, antibody, perturbagen, growth factor, ligand, linked data, organ, disease, data set |
uses: HMS LINCS Database uses: Bioassay Ontology uses: Molecular Libraries Program is related to: Broad Institute is related to: Harvard Medical School; Massachusetts; USA is related to: Columbia University; New York; USA is related to: Yale University; Connecticut; USA is related to: Arizona State University; Arizona; USA has parent organization: University of Miami; Florida; USA |
NHGRI ; NHLBI U01 HL111561 |
PMID:29140462 | Free, Freely available | nlx_158348 | http://dev3.ccs.miami.edu:8080/datasets-beta/ | http://lifekb.org/ | SCR_003937 | lifekb, LIFE LINCS Information Framework | 2026-09-12 01:01:29 | 1 | ||||
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HapMap 3 and ENCODE 3 Resource Report Resource Website 1+ mentions |
HapMap 3 and ENCODE 3 (RRID:SCR_004563) | HapMap 3 and ENCORE 3 | data or information resource, database | Draft release 3 for genome-wide SNP genotyping and targeted sequencing in DNA samples from a variety of human populations (sometimes referred to as the HapMap 3 samples). This release contains the following data: * SNP genotype data generated from 1184 samples, collected using two platforms: the Illumina Human1M (by the Wellcome Trust Sanger Institute) and the Affymetrix SNP 6.0 (by the Broad Institute). Data from the two platforms have been merged for this release. * PCR-based resequencing data (by Baylor College of Medicine Human Genome Sequencing Center) across ten 100-kb regions (collectively referred to as ENCODE 3) in 712 samples. Since this is a draft release, please check this site regularly for updates and new releases. The HapMap 3 sample collection comprises 1,301 samples (including the original 270 samples used in Phase I and II of the International HapMap Project) from 11 populations, listed below alphabetically by their 3-letter labels. Five of the ten ENCODE 3 regions overlap with the HapMap-ENCODE regions; the other five are regions selected at random from the ENCODE target regions (excluding the 10 HapMap-ENCODE regions). All ENCODE 3 regions are 100-kb in size, and are centered within each respective ENCODE region. The HapMap 3 and ENCORE 3 data are downloadable from the ftp site. | human, gene, genotype, sequence, single nucleotide polymorphism, dna, software |
is listed by: 3DVC is related to: NHGRI Sample Repository for Human Genetic Research has parent organization: Baylor University; Texas; USA |
Wellcome Trust ; NHGRI ; NIDCD |
nlx_143820 | http://www.hgsc.bcm.tmc.edu/project-medseq-hm-hapmap3encode3.hgsc?pageLocation=hapmap3encode3 | SCR_004563 | 2026-09-12 01:01:32 | 3 | |||||||
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SGD Resource Report Resource Website 1000+ mentions |
SGD (RRID:SCR_004694) | SGD, SGD LOCUS, SGD REF | data or information resource, database | A curated database that provides comprehensive integrated biological information for Saccharomyces cerevisiae along with search and analysis tools to explore these data. SGD allows researchers to discover functional relationships between sequence and gene products in fungi and higher organisms. The SGD also maintains the S. cerevisiae Gene Name Registry, a complete list of all gene names used in S. cerevisiae which includes a set of general guidelines to gene naming. Protein Page provides basic protein information calculated from the predicted sequence and contains links to a variety of secondary structure and tertiary structure resources. Yeast Biochemical Pathways allows users to view and search for biochemical reactions and pathways that occur in S. cerevisiae as well as map expression data onto the biochemical pathways. Literature citations are provided where available. | database, yeast, pathway, analysis, gene, nomenclature, predicted sequence, fungi, functional relationship, protein structure, bio.tools, FASEB list |
uses: InterMOD is used by: NIF Data Federation is used by: PhenoGO is listed by: re3data.org is listed by: OMICtools is listed by: InterMOD is listed by: bio.tools is listed by: Debian is affiliated with: InterMOD is related to: AmiGO is related to: Yeast Search for Transcriptional Regulators And Consensus Tracking is related to: HomoloGene is related to: TXTGate is related to: PhenoGO has parent organization: Stanford University School of Medicine; California; USA has parent organization: Stanford University; Stanford; California is parent organization of: Ascomycete Phenotype Ontology is parent organization of: SGD Gene Ontology Slim Mapper is organization facet of: Alliance of Genome Resources |
NHGRI 5P41HG001315-11; NHGRI 5P41HG002273-05; NHGRI 5U41HG001315-18; NHGRI 2U41HG002273-13; NHGRI 5R01HG004834-04 |
PMID:24265222 PMID:12519985 PMID:9399804 |
Free for academic use, The community can contribute to this resource, Non-commercial | nif-0000-03456, biotools:sgd, r3d100010419, OMICS_01661 | https://bio.tools/sgd, https://doi.org/10.17616/R3N313 | http://genome-www.stanford.edu/Saccharomyces/ | SCR_004694 | SGD LOCUS, Saccharomyces Genome Database, SGD REF | 2026-09-12 01:01:33 | 1950 | |||
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Ancestrymap Resource Report Resource Website 10+ mentions |
Ancestrymap (RRID:SCR_004353) | ANCESTRYMAP | software application, software resource, source code | Software application that finds skews in ancestry that are potentially associated with disease genes in recently mixed populations like African Americans. It can be downloaded for either UNIX or Linux. | disease gene, ancestry, gene, genomic, unix, linux, admixture mapping, admixture, genome, linkage disequilibrium, population |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools has parent organization: Harvard Medical School; Massachusetts; USA |
Burroughs Wellcome Fund ; NHGRI K-01 HG002758-01 |
PMID:15088269 | Restricted | nlx_39116, biotools:ancestrymap, OMICS_02083 | https://reich.hms.harvard.edu/software, https://bio.tools/ancestrymap | http://genepath.med.harvard.edu/~reich/Software.htm, http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html | SCR_004353 | 2026-09-12 01:01:31 | 12 | ||||
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International Knockout Mouse Consortium Resource Report Resource Website 50+ mentions |
International Knockout Mouse Consortium (RRID:SCR_005574) | IKMC | data or information resource, database | Database of the international consortium working together to mutate all protein-coding genes in the mouse using a combination of gene trapping and gene targeting in C57BL/6 mouse embryonic stem (ES) cells. Detailed information on targeted genes is available. The IKMC includes the following programs: * Knockout Mouse Project (KOMP) (USA) ** CSD, a collaborative team at the Children''''s Hospital Oakland Research Institute (CHORI), the Wellcome Trust Sanger Institute and the University of California at Davis School of Veterinary Medicine , led by Pieter deJong, Ph.D., CHORI, along with K. C. Kent Lloyd, D.V.M., Ph.D., UC Davis; and Allan Bradley, Ph.D. FRS, and William Skarnes, Ph.D., at the Wellcome Trust Sanger Institute. ** Regeneron, a team at the VelociGene division of Regeneron Pharmaceuticals, Inc., led by David Valenzuela, Ph.D. and George D. Yancopoulos, M.D., Ph.D. * European Conditional Mouse Mutagenesis Program (EUCOMM) (Europe) * North American Conditional Mouse Mutagenesis Project (NorCOMM) (Canada) * Texas A&M Institute for Genomic Medicine (TIGM) (USA) Products (vectors, mice, ES cell lines) may be ordered from the above programs. | gene, knock out mouse, chromosome, allele, c57bl/6, embryonic stem cell, vector, mutant, es cell, genome, targeting, gene list, FASEB list |
is related to: Texas A and M Institute for Genomic Medicine is related to: European Mouse Mutant Archive is related to: CMMR - Canadian Mouse Mutant Repository is parent organization of: EUCOMMTOOLS is parent organization of: North American Conditional Mouse Mutagenesis Project is parent organization of: European Conditional Mouse Mutagenesis Program is parent organization of: Knockout Mouse Project |
European Union ; NHGRI HG004074 |
PMID:22968824 PMID:21677750 |
nlx_146200 | SCR_005574 | 2026-09-12 01:01:38 | 68 | |||||||
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SNPRelate Resource Report Resource Website 10+ mentions |
SNPRelate (RRID:SCR_022719) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-12 01:00:28 | 13 | ||||||||
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hifiasm-meta Resource Report Resource Website 1+ mentions |
hifiasm-meta (RRID:SCR_022771) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-12 01:00:29 | 2 | ||||||||
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ComplexUpset Resource Report Resource Website 10+ mentions |
ComplexUpset (RRID:SCR_022752) | data analysis software, data processing software, software application, software resource | 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 |
Air Force Research Laboratory and DARPA ; Austrian Science Fund ; NHGRI K99 HG007583 |
PMID:26356912 | Free, Available for download, Freely available | SCR_022752 | 2026-09-12 01:00:29 | 25 | ||||||||
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sei Resource Report Resource Website 10+ 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 | 2026-09-12 01:00:27 | 10 | ||||||||
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UpSet Resource Report Resource Website 10+ mentions |
UpSet (RRID:SCR_022731) | data analysis software, data processing software, data visualization software, software application, 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 | Air Force Research Laboratory ; Austrian Science Fund ; DARPA ; NHGRI K99 HG007583 |
PMID:26356912 | Free, Available for download, Freely available | https://github.com/VCG/upset | SCR_022731 | UpSet Plot | 2026-09-12 01:00:28 | 16 | |||||||
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SvABA Resource Report Resource Website 10+ mentions |
SvABA (RRID:SCR_022998) | data analysis software, data processing software, sequence analysis software, software application, 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 | Broad Institute ; DFCI-Novartis Drug Discovery Program ; NCI R01CA188228; NCI U54CA143798; NHGRI T32 HG002295; Pediatric Low-Grade Astrocytoma Foundation ; Voices Against Brain Cancer ; Wellcome Fund Career Award for Medical Scientists |
PMID:29535149 | Free, Available for download, Freely available | SCR_022998 | 2026-09-12 01:00:31 | 18 | |||||||||
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UpSetPlot Resource Report Resource Website 1+ mentions |
UpSetPlot (RRID:SCR_023225) | data processing software, data visualization software, software application, software resource | Software Python implementation of UpSet plots to visualize set overlaps. | UpSet plots, Python, visualize set overlaps, | Air Force Research Laboratory ; Austrian Science Fund ; DARPA ; NHGRI K99 HG007583 |
PMID:26356912 | Free, Available for download, Freely available | SCR_023225 | 2026-09-12 01:00:37 | 7 | |||||||||
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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 | Agence Nationale pour la Recherche ; California Institute of Regenerative Medicine GC1R-06673C; Fondation pour la Recherche Médicale DEQ20140329544; MRC 53658; NCI U54 HG007990; NHGRI U41 HG002371; NIH Office of the Director U42 OD011174 |
PMID:27380939 | Free, Available for download | https://github.com/maximilianh/crisporWebsite | SCR_015935 | 2026-09-12 01:00:35 | 1658 | |||||||
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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 |
Brain and Behavior Research Foundation ; California Institute for Regenerative Medicine ; Chan Zuckerberg Initiative Foundation ; NHGRI 1U41HG010972; NHGRI 5R01HG010329; NHGRI 5U41HG002371; NIMH DP2MH122400; NIMH RF1MH121268; NIMH U01MH114825; NINDS K99 NS111731; Silicon Valley Community Foundation ; Simons Foundation ; University of California Office of the President Emergency COVID-19 Research Seed Funding |
PMID:34244710 | Free, Freely available | https://cellbrowser.readthedocs.io/en/master/, https://github.com/maximilianh/cellBrowser | SCR_023293 | 2026-09-12 01:00:37 | 155 | |||||||
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HetMatPy Resource Report Resource Website 1+ mentions |
HetMatPy (RRID:SCR_023409) | data analysis software, data processing software, network analysis software, software application, 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 ; NCI R01 CA237170; NHGRI R01 HG010067 |
PMID:36711546 | Free, Available for download, Freely available | SCR_023409 | hetmatpy | 2026-09-12 01:00:38 | 1 | ||||||||
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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 | 2026-09-12 01:00:38 | 18 | ||||||||
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NCGC Pharmaceutical Collection Resource Report Resource Website 1+ mentions |
NCGC Pharmaceutical Collection (RRID:SCR_006909) | NPC | material resource, reagent supplier | The NCGC Pharmaceutical Collection (NPC) is a comprehensive, publically-accessible collection of approved and investigational drugs for high-throughput screening that provides a valuable resource for both validating new models of disease and better understanding the molecular basis of disease pathology and intervention. The NPC has already generated several useful probes for studying a diverse cross section of biology, including novel targets and pathways. NCGC provides access to its set of approved drugs and bioactives through the Therapeutics for Rare and Neglected Diseases (TRND) program and as part of the compound collection for the Tox21 initiative, a collaborative effort for toxicity screening among several government agencies including the US Environmental Protection Agency (EPA), the National Toxicology Program (NTP), the US Food and Drugs Administration (FDA), and the NCGC. Of the nearly 2750 small molecular entities (MEs) that have been approved for clinical use by US (FDA), EU (EMA), Japanese (NHI), and Canadian (HC) authorities and that are amenable to HTS screening, we currently possess 2,400 as part of our screening collection. The NPC resource currently consists of (i) the physical collection suitable for high throughput screening (HTS) and (ii) the informatics browser and database. Putting together the physical collection has been surprisingly challenging in terms of the time and effort required in the informatics, compound management and synthetic chemistry related activities required for this endeavor. We provide access to the NPC screening library through collaboration. Please contact our Scientific Director Dr. Chris Austin for additional information. The other half of the NPC resource is the NPC browser. This is a self-contained software that is actively developed and maintained by the informatics group to provide electronic access to the NPC content. The latest version of the NPC browser for various platforms can be downloaded. | drug, disease, high-throughput screening, molecule, molecular entity, compound, small molecule | has parent organization: NIH Chemical Genomics Center | NHGRI | PMID:21525397 | nlx_144647 | SCR_006909 | The NCGC Pharmaceutical Collection, National Center for Advancing Translational Sciences Pharmaceutical Collection, NIH Chemical Genomics Center Pharmaceutical Collection, National Institutes of Health Chemical Genomics Center Pharmaceutical Collection, NCATS Pharmaceutical Collection | 2026-09-12 01:00:57 | 5 | ||||||
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OwlSim Resource Report Resource Website 1+ mentions |
OwlSim (RRID:SCR_006819) | OwlSim | data processing software, software application, software resource | Software package that provides the ability to do a number of standard semantic similarity methods and includes novel methods for combining these with dynamic selection of anonymous grouping classes. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | functional similarity, semantic similarity, ontology, phenotype, annotation, windows, mac os x, linux, unix |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Berkeley Bioinformatics Open-Source Projects has parent organization: OWLTools |
Biomedical Information Science and Technology Initiative ; National Center for Biomedical Ontology ; NHGRI U54 HG004028; NHGRI HG002659 |
PMID:19956802 | Open unspecified license - Free for academic use | nlx_149312 | SCR_006819 | 2026-09-12 01:00:57 | 5 | ||||||
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Phenex Resource Report Resource Website 1+ mentions |
Phenex (RRID:SCR_021748) | software resource | Software application for annotating character matrix files with ontology terms. Character states can be annotated using Entity-Quality syntax, where entity, quality, and possibly related entities are drawn from requisite ontologies. In addition, taxa (the rows of a character matrix) can be annotated with identifiers from taxonomy ontology. Phenex saves ontology annotations alongside original free text character matrix data using new NeXML format standard for evolutionary data. | phenotype, ontology, taxonomy ontology, taxa, ontology annotations, free text character matrix data, NeXML, evolutionary data | NHGRI HG002659; NSF DBI 0641025; NSF EF0423641 |
DOI:10.1371/journal.pone.0010500 | Free, Available for download, Freely available | https://github.com/phenoscape/Phenex/wiki#download--installation | SCR_021748 | 2026-09-12 01:00:01 | 1 | ||||||||
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ntCard Resource Report Resource Website 1+ mentions |
ntCard (RRID:SCR_022010) | software resource | Software tool for estimating k-mer coverage histogram of genomics data. Streaming algorithm for estimating frequencies of k-mers in genomics datasets. | K-mer, estimating k-mer coverage histogram, genomics data, estimating frequencies of k-mers | British Columbia Cancer Foundation ; Genome British Columbia ; Genome Canada ; NHGRI R01 HG007182 |
DOI:10.1093/bioinformatics/btw832 | Free, Available for download, Freely available | https://github.com/bcgsc/ntCard | SCR_022010 | 2026-09-12 01:00:04 | 1 |
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