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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Mouse Genome Database Resource Report Resource Website 500+ mentions |
Mouse Genome Database (RRID:SCR_012953) | MGD | data or information resource, database | Community model organism database for laboratory mouse and authoritative source for phenotype and functional annotations of mouse genes. MGD includes complete catalog of mouse genes and genome features with integrated access to genetic, genomic and phenotypic information, all serving to further the use of the mouse as a model system for studying human biology and disease. MGD is a major component of the Mouse Genome Informatics.Contains standardized descriptions of mouse phenotypes, associations between mouse models and human genetic diseases, extensive integration of DNA and protein sequence data, normalized representation of genome and genome variant information. Data are obtained and integrated via manual curation of the biomedical literature, direct contributions from individual investigators and downloads from major informatics resource centers. MGD collaborates with the bioinformatics community on the development and use of biomedical ontologies such as the Gene Ontology (GO) and the Mammalian Phenotype (MP) Ontology. | gene, genome, genetic, chromosome, clone, cytogenetic, dna, genomic, inbred, mammalian, mouse, mutant, ortholog, phenotype, primer, protein, reagent, sequence, strain, bio.tools |
is used by: DisGeNET is listed by: Debian is listed by: bio.tools is related to: Mouse Genome Informatics (MGI) has parent organization: Jackson Laboratory |
NHGRI HG000330 | PMID:21051359 | biotools:mgi, biotools:mgd, nif-0000-10301 | http://www.informatics.jax.org/mgihome/projects/overview.shtml, https://bio.tools/mgd, https://bio.tools/mgi | SCR_012953 | Mouse Genome Informatics: Mouse Genome Database, MGID, Mouse Genome Informatics Database | 2026-07-28 09:43:09 | 502 | |||||
|
HumanBase Resource Report Resource Website 50+ mentions |
HumanBase (RRID:SCR_016145) | data or information resource, database | Formerly known as GIANT (Genome-scale Integrated Analysis of gene Networks in Tissues), HumanBase applies machine learning algorithms to learn biological associations from massive genomic data collections. These integrative analyses reach beyond existing "biological knowledge" represented in the literature to identify novel, data-driven associations. | genome, analysis, tissue, network, gene, machine, learning, biology | NIGMS R01 GM071966; NHGRI R01 HG005998; NHLBI U54 HL117798; NIGMS P20 GM103534; NHGRI T32 HG003284; NCI T32 CA009528; NIGMS P50 GM071508; US Department Of Health And Human Services HHSN272201000054C |
PMID:25915600 | Free, Public | SCR_016145 | GIANT (Genome-scale Integrated Analysis of gene Networks in Tissues), GIANT | 2026-07-28 09:44:06 | 74 | ||||||||
|
TheCellMap Resource Report Resource Website 10+ mentions |
TheCellMap (RRID:SCR_018728) | data or information resource, service resource, database | Web accessible database for visualizing and mining global yeast genetic interaction network. Allows users to easily access, visualize, explore, and functionally annotate genetic interactions, or to extract and reorganize sub networks, using data driven network layouts in intuitive and interactive manner. Used for storing and visualizing genetic interactions in S. cerevisiae. | Genetic interactions, genetic network, yeast genetics, synthetic genetic array, network visualization, annotation, data, genetic interaction visualization | has parent organization: University of Toronto; Ontario; Canada | NHGRI R01 HG005853; NHGRI R01 HG005084; Canadian Institutes of Health Research ; NSF DBI 0953881 |
PMID:28325812 | Free, Freely available | SCR_018728 | TheCellMap.org | 2026-07-28 09:44:48 | 34 | |||||||
|
PhenoDB Resource Report Resource Website 1+ mentions |
PhenoDB (RRID:SCR_016551) | data or information resource, database | Database for phenotype genotype associations for humans. Used by clinical researchers to store standardized phenotypic information, diagnosis, and pedigree data and then run analyses on VCF files from individuals, families or cohorts with suspected Mendelian disease. | store, standardized, phenotype, genotype, Mendelian disease, mutation, next, generation, sequencing, data | has parent organization: Johns Hopkins University School of Medicine; Baltimore, Maryland; USA | Mendelian disease | NHGRI | PMID:25684268 | Free, Registration required, Freely available for non commercial users | SCR_016551 | 2026-07-28 09:44:17 | 5 | |||||||
|
RegulomeDB Resource Report Resource Website 100+ mentions |
RegulomeDB (RRID:SCR_017905) | data or information resource, service resource, database | Database that annotates SNPs with known and predicted regulatory elements in intergenic regions of H. sapiens genome. Known and predicted regulatory DNA elements include regions of DNAase hypersensitivity, binding sites of transcription factors, and promoter regions that have been biochemically characterized to regulation transcription. Source of these data include public datasets from GEO, ENCODE project, and published literature. | Annotate, SNP, regulatory, DNA, element, intergenic, region, human, genome, sequence, DNAase, hypersensitivity, binding, site, transcription, factor, promoter, region, data, FASEB list | NHGRI U54 HG 004558; Beta Cell Consortium |
PMID:22955989 | Free, Freely available | SCR_017905 | 2026-07-28 09:44:39 | 123 | |||||||||
|
Adaptive Shrinkage in R Resource Report Resource Website 1+ mentions |
Adaptive Shrinkage in R (RRID:SCR_023486) | ashr | software toolkit, software resource | Software R package for adaptive shrinkage. Implements Empirical Bayes approach for large scale hypothesis testing and false discovery rate estimation. | adaptive shrinkage, large scale hypothesis testing, false discovery rate estimation, | NHGRI HG02585; Gordon and Betty Moore Foundation |
PMID:27756721 | Free, Available for download, Freely available | SCR_023486 | 2026-07-28 09:45:56 | 8 | ||||||||
|
MR-PRESSO Resource Report Resource Website 50+ mentions |
MR-PRESSO (RRID:SCR_023697) | software toolkit, software resource | Software R package for performing Mendelian randomization pleiotropy residual sum and outlier method.Used to identify horizontal pleiotropic outliers in multi instrument summary level MR testing. | Mendelian randomization, identify horizontal pleiotropic outliers, multi instrument summary level MR testing, | NIGMS R35 GM124836; NHLBI R01 HL139865; AstraZeneca ; Goldfinch Bio ; American Heart Association Cardiovascular Genome Phenome Discovery ; NIMH 1R01 MH094469; NIMH 1R01 MH107649; NHGRI 5U01 HG009088 |
PMID:29686387 | Free, Available for download, Freely available | SCR_023697 | Mendelian Randomization Pleiotropy RESidual Sum and Outlier | 2026-07-28 09:45:57 | 64 | ||||||||
|
Dfam Resource Report Resource Website 50+ mentions |
Dfam (RRID:SCR_021168) | data or information resource, database | Open collection of Transposable Element DNA sequence alignments, hidden Markov Models, consensus sequences, and genome annotations.Dfam 3.2 provides early access to uncurated, de novo generated families. | Transposable Element, DNA sequence alignments, hidden Markov Models, consensus sequences, genome annotations | is related to: RepeatModeler | NHGRI U24 HG010136; NHGRI R01 HG002939 |
DOI:10.1186/s13100-020-00230-y | Free, Freely available | SCR_021168 | Dfam 3.2 | 2026-07-28 09:45:03 | 82 | |||||||
|
Eagle Resource Report Resource Website 50+ mentions |
Eagle (RRID:SCR_015991) | software toolkit, software resource | Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods. | hmm, hidden markov model, statistic, estimation, haplotype, phase, reference, panel, sequencing, algorithm, analysis, probability |
is listed by: Debian is listed by: OMICtools has parent organization: Broad Institute |
NHGRI R01 HG006399; NIMH R01 MH101244; NHGRI F32HG007805; Wellcome Trust WT098051; Austrian Science Fund J-3401; NHGRI HG007022; NHLBI HL117626; Fannie and John Hertz Foundation ; NCRR S10 RR028832; NWO 480-05-003; Dutch Brain Foundation |
PMID:27694958 PMID:27270109 |
Free, Available for download, Freely available | OMICS_14099, SCR_017262 | https://sources.debian.org/src/bio-eagle/, https://github.com/poruloh/Eagle, https://data.broadinstitute.org/alkesgroup/Eagle/downloads/ | SCR_015991 | Bio-eagle, Eagle1, Eagle2 | 2026-07-28 09:44:05 | 51 | |||||
|
rtracklayer Resource Report Resource Website 10+ mentions |
rtracklayer (RRID:SCR_021325) | software toolkit, software resource | Software R package for interfacing with genome browsers.Supports integration of existing genome browsers with experimental data analyses performed in R. R interface to genome annotation files and UCSC genome browser. | Existing genome browsers integration, genome annotation files interface, interfacing with genome browsers | NHGRI P41 HG004059 | PMID:19468054 | Free, Available for download, Freely available | https://github.com/lawremi/rtracklayer | SCR_021325 | 2026-07-28 09:45:10 | 19 | ||||||||
|
Mash Resource Report Resource Website 50+ mentions |
Mash (RRID:SCR_019135) | software application, data analytics software, software resource | Software tool for genome and metagenome distance estimation using MinHash. Reduces large sequences and sequence sets to small, representative sketches, from which global mutation distances can be rapidly estimated. | Genome distance estimation, metagenome distance estimation, MinHash, mutation distance, sequence, sequence set |
is listed by: Debian is listed by: OMICtools |
NHGRI ; NIH |
PMID:27323842 | Free, Available for download, Freely available | OMICS_10468 | https://mash.readthedocs.io/en/latest/, https://sources.debian.org/src/mash/ | SCR_019135 | 2026-07-28 09:44:56 | 54 | ||||||
|
PhenStat Resource Report Resource Website 1+ mentions |
PhenStat (RRID:SCR_021317) | software application, data analysis software, software resource, data processing software, software toolkit | Software R package for statistical analysis of phenotypic data.Tool kit for standardized analysis of high throughput phenotypic data. | Statistical analysis, phenotypic data, standardized analysis, bio.tools, Bioconductor |
is listed by: Bioconductor is listed by: bio.tools |
Wellcome Trust ; NHGRI U54 HG006370 |
PMID:26147094 | Free, Available for download, Freely available | biotools:phenstat | https://bio.tools/phenstat | SCR_021317 | 2026-07-28 09:45:17 | 8 | ||||||
|
LocusZoom.org Resource Report Resource Website 10+ mentions |
LocusZoom.org (RRID:SCR_021374) | software resource, data access protocol, web service | Web tool to investigate genome wide association results in their local genomic context. Adds new features to LocusZoom such as Manhattan plots, annotation options, and calculations that put findings in context. Used for interactive and embeddable visualization of genetic association study results.Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources. | Generate interactive plots, shareable plots, GWAS summary statistics, visualizing statistical genetic data, genetic association study | NHGRI HG009976; NIH BOEH15AMP |
DOI:10.1093/bioinformatics/btab186 | Free, Freely available | SCR_021374 | LocusZoom.js | 2026-07-28 09:45:11 | 32 | ||||||||
|
CRISPResso Resource Report Resource Website 10+ mentions |
CRISPResso (RRID:SCR_021538) | software application, data analysis software, sequence analysis software, software resource, data processing software, software toolkit | Software suite of tools to qualitatively and quantitatively evaluate outcomes of genome editing experiments in which target loci are subject to deep sequencing and provides integrated, user friendly interface. Used for analysis of CRISPR-Cas9 genome editing outcomes from sequencing data. CRISPResso2 provides accurate and rapid genome editing sequence analysis.Used for analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments. | Quantification, visualization, CRISPR-Cas9 outcomes, coding sequences evaluation, noncoding elements evaluation, selected off target sites evaluation, genome editing evaluation. | NHGRI RM1 HG009490; NIBIB R01 EB022376; NIGMS R35 GM118062; NIGMS R35 GM118158; NIDDK R03 DK109232; NHLBI P01 HL32262; NHGRI R00 HG008399; NIDDK P30 DK049216; NHLBI R01 HL119099; NHGRI R01 HG005085 |
PMID:27404874 PMID:30809026 |
Free, Available for download, Freely available | https://github.com/pinellolab/CRISPResso2, https://github.com/pinellolab/CRISPResso | SCR_021538 | CRISPResso2 | 2026-07-28 09:45:25 | 21 | |||||||
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SALSA Resource Report Resource Website 10+ mentions |
SALSA (RRID:SCR_022013) | software application, software resource, data analysis software, data processing software | Software tool for scaffold long read assemblies with Hi-C data. | scaffolding, Hi-C data, scaffold long read assemblies | NHGRI R44 HG009584; NIAID R01 AI100947; Ministry of Health and Welfare ; Republic of Korea |
DOI:10.1371/journal.pcbi.1007273 DOI:10.1186/s12864-017-3879-z |
Free, Available for download, Freely available | SCR_022013 | SALSA2 | 2026-07-28 09:45:23 | 40 | ||||||||
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LongReadSum Resource Report Resource Website 1+ mentions |
LongReadSum (RRID:SCR_026408) | software application, source code, software resource | Software fast and flexible QC and signal summarization tool for long read sequencing data. | signal summarization, quality control, long read sequencing data, | NHGRI F31HG013259; NHGRI HG013359; NIGMS GM132713 |
PMID:39211184 | Free, Available for download, Freely available, | SCR_026408 | 2026-07-28 09:46:38 | 1 | |||||||||
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GenomicKB Resource Report Resource Website |
GenomicKB (RRID:SCR_026591) | knowledge base, data or information resource, database, knowledge graph | Database that uses knowledge graph to consolidate genomic datasets and annotations. Graph database for researchers to explore and investigate human genome, epigenome, transcriptome, and 4D nucleome. Genomic entities and relationships are represented as diverse nodes and edges with properties. | genomic datasets and annotations, human genome, epigenome, transcriptome, 4D nucleome, | NHGRI R35HG011279 | PMID:36318240 | Free, Freely available | SCR_026591 | Genomic Knowledgebase | 2026-07-28 09:46:43 | 0 | ||||||||
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Bigtools Resource Report Resource Website |
Bigtools (RRID:SCR_026627) | software resource, source code, software toolkit, software library | Software library and associated tools for reading and writing bigwig and bigbed files. High-performance BigWig and BigBed library in Rust. | BigWig, BigBed, Rust, reading and writing bigwig and bigbed files, | NHGRI UM1 HG011536 | PMID:38837370 | Free, Available for download, Freely available | SCR_026627 | 2026-07-28 09:46:42 | 0 | |||||||||
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chromvar Resource Report Resource Website 10+ mentions |
chromvar (RRID:SCR_026570) | software application, data analysis software, source code, software resource, data processing software, software toolkit | Software R package for analyzing sparse chromatin-accessibility data by estimating gain or loss of accessibility within peaks sharing the same motif or annotation while controlling for technical biases. Enables accurate clustering of scATAC-seq profiles and characterization of known and de novo sequence motifs associated with variation in chromatin accessibility. Used for analysis of sparse chromatin accessibility data from single cell or bulk ATAC or DNAse-seq data. | analyzing sparse chromatin-accessibility data, analysis of sparse chromatin accessibility data, single cell, bulk ATAC, DNAse-seq data, | is used by: pychromVAR | NHGRI P50HG007735; NIAID U19AI057266; Rita Allen Foundation ; Harvard Society of Fellows ; Broad Institute Fellowship |
PMID:28825706 | Free, Available for download, Freely available | SCR_026570 | chromatin Variability Across Regions | 2026-07-28 09:46:41 | 11 | |||||||
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Borzoi Resource Report Resource Website 1+ mentions |
Borzoi (RRID:SCR_026619) | source code, software toolkit, software resource | Software package to access the Borzoi models, which are convolutional neural networks trained to predict RNA-seq coverage at 32bp resolution given 524kb input sequences. | Borzoi models access, convolutional neural networks, predict RNA-seq coverage, | Common Fund of the Office of the Director ; NCI ; NHGRI ; NHLBI ; NIDA ; NIMH ; NINDS |
PMID:39779956 | Free, Available for download, Freely available | SCR_026619 | 2026-07-28 09:46:43 | 1 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
