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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SnapATAC2 Resource Report Resource Website 1+ mentions |
SnapATAC2 (RRID:SCR_026622) | software resource, software toolkit, source code | Software Python/Rust package for single-cell epigenomics analysis. | Single-cell epigenomics analysis, | NHGRI U01HG012059; NHGRI UM1HG011585; NIMH RF1MH128838; NIMH UM1MH130994; NIA R24AG073198; NIMH U01MH114828; NIA R56AG069107; NIA U54AG079758; NIMH U01MH121282; NIMH U19MH114831; NEI R01EY031663 |
PMID:38191932 | Free, Available for download, Freely available | SCR_026622 | 2026-08-04 09:46:02 | 3 | |||||||||
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HiGlass Resource Report Resource Website 10+ mentions |
HiGlass (RRID:SCR_026687) | web application, software resource, source code | Web-based visual exploration and analysis of genome interaction maps. | visual exploration and analysis, genome interaction maps, | NCI U01CA200059; NHGRI R00 HG007583; NHGRI U54 HG007963 |
PMID:30143029 | Free, Available for download, Freely available | SCR_026687 | 2026-08-04 09:46:03 | 45 | |||||||||
|
apeglm Resource Report Resource Website |
apeglm (RRID:SCR_026951) | software resource, software toolkit | Software package provides Bayesian shrinkage estimators for effect sizes for variety of GLM models, using approximation of posterior for individual coefficients. | Bayesian shrinkage estimators, | NHGRI R01 HG009125; NCI P01 CA142538; NIEHS P30 ES010126; NIGMS R01 GM070335 |
PMID:30395178 | Free, Available for download, Freely available, | SCR_026951 | , Approximate Posterior Estimation for generalized linear model, Approximate posterior estimation for GLM | 2026-08-04 09:46:06 | 0 | ||||||||
|
dREG Resource Report Resource Website 1+ mentions |
dREG (RRID:SCR_027012) | software application, software resource, source code | Software tool for detecting regulatory elements using GRO-seq and PRO-seq. | detecting regulatory elements, GRO-seq, PRO-seq | NHGRI 5R01HG007070; NIDDK R01 DK058110 |
PMID:25799441 | Free, Available for download, Freely available | SCR_027012 | 2026-08-04 09:46:08 | 1 | |||||||||
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PHATE Resource Report Resource Website 1+ mentions |
PHATE (RRID:SCR_027119) | data processing software, source code, software resource, software application, 3d visualization software, data visualization software | Software tool for visualizing high dimensional data using novel conceptual framework for learning and visualizing manifold to preserve both local and global distances. | visualizing high dimensional data, high dimensional data, | NICHD F31HD097958; NHGRI 1R01HG008383; NSF ; NIGMS R01GM107092; NIGMS R01GM130847 |
PMID:31796933 | Free, Available for download, Freely available, | SCR_027119 | Potential of Heat-diffusion for Affinity-based Transition Embedding | 2026-08-04 09:46:08 | 2 | ||||||||
|
TEProf3 Resource Report Resource Website |
TEProf3 (RRID:SCR_027288) | software resource, software toolkit, source code | Software pipeline to detect Transposable Elements transcripts. Used to identify TE-derived promoters and transcripts using transcriptomic data from multiple sources, including short-read RNA-seq data, long-read RNA-seq data and single cell RNA-seq data. | Transposable Elements, Transposable Elements transcripts, detect TE transcripts, transcriptomic data, short-read RNA-seq data, long-read RNA-seq data, single cell RNA-seq data, | NHGRI R01HG007175; NIA R01AG078958; NINDS U24NS132103; NHGRI U01HG013227 |
PMID:40360186 | Free, Available for download, Freely available, | SCR_027288 | , TE-derived Promoter Finder 3 | 2026-08-04 09:46:10 | 0 | ||||||||
|
Current Topics in Genome Analysis Resource Report Resource Website |
Current Topics in Genome Analysis (RRID:SCR_006475) | CTGA | topical portal, portal, training resource, data or information resource | Current Topics in Genome Analysis lecture series consists of 13 lectures on successive Wednesdays, with a mixture of local and outside speakers covering the major areas of genomics. In this tenth edition of the series, rather than splitting the lectures into laboratory-based and computationally-based blocks, we have intermingled the lectures by general subject area. We hope that this approach conveys the idea that both laboratory- and computationally-based approaches are necessary in order to do cutting-edge biological research in the future. The lectures are geared at the level of first year graduate students, are practical in nature, and are intended for a diverse audience. Handouts will be provided for each lecture, and time will be available at the end of each lecture for questions and discussion. All lectures are held on Wednesday mornings from 9:30 a.m. to 11:00 a.m. in the Lipsett Amphitheatre of the National Institutes of Health Clinical Center (Building 10). Course Directors: Andy Baxevanis, Ph.D., Eric Green, M.D., Ph.D., Tyra Wolfsberg, Ph.D. Lectures in this series will be available on the GenomeTV channel of YouTube viewing shortly after the live lecture and also includes all of the handouts. Lectures will not be Webcast live. The lecture series archives (available from 2005-) covers important milestones in genetics. CME Credits: This activity has been approved for AMA PRA Category 1 Credits. The intended audience includes clinicians, clinical geneticists, social and behavioral scientists, genetic counselors, those involved with genetics and public policy, health educators, and other biomedical and clinical scientists with an interest in genetics, genomics and personalized medicine. No prior expertise on the part of the audience will be required and the lecturers will be instructed to provide any relevant background as part of their lectures. | genomics, bioinformatics, lecture, genome analysis | has parent organization: National Human Genome Research Institute | NHGRI | http://www.genome.gov/COURSE2012 | SCR_006475 | Current Topics in Genome Analysis 2012, Current Topics in Genome Analysis lecture series, NHGRI: Current Topics in Genome Analysis | 2026-08-04 09:41:37 | 0 | |||||||
|
scHiCluster Resource Report Resource Website |
scHiCluster (RRID:SCR_027854) | software resource, software toolkit | Software Python package for single-cell chromosome contact data analysis. It includes the identification of cell types (clusters), loop calling in cell types, and domain and compartment calling in single cells. Facilitates visualization and comparison of single-cell 3D genomes. | single-cell chromosome contact data analysis, single-cell, chromosome, contact, data analysis, | NHGRI R21 HG009274 | PMID:31235599 | Free, Available for download, Freely Available | SCR_027854 | 2026-08-04 09:46:18 | 0 | |||||||||
|
tximeta Resource Report Resource Website |
tximeta (RRID:SCR_028005) | software resource, software toolkit | Software R package for reference sequence checksums for provenance identification in RNA-seq. Performs numerous annotation and metadata gathering tasks on behalf of users during the import of transcript counts and abundance from quantification tools such as salmon. Data are imported as SummarizedExperiment objects with associated GenomicRanges metadata. Correct metadata is added automatically via reference sequence digests, facilitating genomic analyses and assisting in computational reproducibility. | reference sequence checksums, provenance identification in RNA-seq, numerous annotation, metadata gathering, | NHGRI R01 HG009937; NIMH R01 MH118349; NCI P01 CA142538; NIEHS P30 ES010126; NHGRI U41 HG004059 |
PMID:32097405 | Free, Available for download, Freely available | SCR_028005 | Tximeta | 2026-08-04 09:46:20 | 0 | ||||||||
|
somalier Resource Report Resource Website |
somalier (RRID:SCR_028167) | software application, software resource | Software application for rapid relatedness estimation for cancer and germline studies using efficient genome sketches extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF. Used for rapid relatedness estimation for cancer and germline studies using efficient genome sketches. | rapid relatedness estimation, cancer and germline studies, efficient genome sketches, quality control, | NHGRI R41HG010126; NHGRI R01HG009141; NCI U24CA209999; NCI R37CA246183; NCI P30CA04014 |
PMID:32664994 | Free, Available for download, Freely available | SCR_028167 | Somalier | 2026-08-04 09:46:25 | 0 | ||||||||
|
MAPP Resource Report Resource Website 50+ mentions |
MAPP (RRID:SCR_010775) | MAPP | software resource | Java program that predicts the impact of all possible amino acid substitutions on the function of the protein., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools has parent organization: Stanford University; Stanford; California |
NHGRI | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00132 | SCR_010775 | Multivariate Analysis of Protein Polymorphism, Multivariate Analysis of Protein Polymorphism:MAPP | 2026-08-01 12:03:57 | 58 | |||||||
|
PHAST Resource Report Resource Website 50+ mentions |
PHAST (RRID:SCR_003204) | PHAST | software resource | A freely available software package for comparative and evolutionary genomics that consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations. For the most part, PHAST focuses on two kinds of applications: the identification of novel functional elements, including protein-coding exons and evolutionarily conserved sequences; and statistical phylogenetic modeling, including estimation of model parameters, detection of signatures of selection, and reconstruction of ancestral sequences. It consists of over 60,000 lines of C code. | evolutionary genomic, evolution, genomics, sequence alignment, phylogenetic tree, genomic annotation, functional element, protein-coding exon, conserved sequence, phylogenetic modeling, ancestral sequence, c |
is listed by: OMICtools is listed by: Debian has parent organization: Cornell University; New York; USA |
NIH ; David and Lucile Packard Foundation ; NHGRI ; University of California Biotechnology Research and Education Program ; NSF DBI-0644111; NIGMS R01-GM082901-01 |
PMID:21278375 DOI:10.1093/bib/bbq072 |
Free, Available for download, Freely available | OMICS_01557 | https://sources.debian.org/src/phast/ | SCR_003204 | Phylogenetic Analysis with Space/Time Models | 2026-08-01 12:02:28 | 58 | ||||
|
ASprofile Resource Report Resource Website 10+ mentions |
ASprofile (RRID:SCR_001833) | ASprofile | software resource | A suite of programs for extracting, quantifying and comparing alternative splicing (AS) events from RNA-seq data. | alternative splicing event, rna-seq, alternative splicing |
is listed by: OMICtools has parent organization: Johns Hopkins University; Maryland; USA |
NHGRI R01-HG006677 | PMID:24555089 | Free, Available for download, Freely available | OMICS_01942 | SCR_001833 | 2026-08-01 12:01:37 | 37 | ||||||
|
Consed Resource Report Resource Website 500+ mentions |
Consed (RRID:SCR_005650) | Consed | software resource | A graphical tool for sequence finishing (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit, and Align Reads To Reference Sequence) | next-generation sequencing, graphical editor, linux, macosx, solaris, c++ |
is listed by: OMICtools has parent organization: University of Washington; Seattle; USA |
NIH ; NHGRI R01HG005710 |
PMID:23995391 PMID:9521923 |
Free for academic use, Free for non-profit use, Commercial license | OMICS_00879 | SCR_005650 | 2026-08-01 12:02:56 | 595 | ||||||
|
JBrowse Resource Report Resource Website 10+ mentions |
JBrowse (RRID:SCR_001004) | JBrowse | software resource | A high-performance visualization tool for interactive exploration of large, integrated genomic datasets written primarily in JavaScript. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations. | genome |
is used by: Genome Resources for Yeast Chromosomes is listed by: OMICtools is listed by: Debian has parent organization: Broad Institute |
NHGRI 5R01HG004483-09 | PMID:22517427 PMID:21221095 |
GNU Lesser General Public License, Account required | OMICS_00918 | https://sources.debian.org/src/jbrowse/ | SCR_001004 | 2026-08-01 12:01:29 | 32 | |||||
|
Consensus Measures for Phenotype and Exposure Resource Report Resource Website 1+ mentions |
Consensus Measures for Phenotype and Exposure (RRID:SCR_006688) | PhenX | knowledge environment | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on 05 01 2025. PhenX is a project to prioritize Phenotype and eXposure measures for Genome-wide Association Studies (GWAS). Leaders of the scientific community will assess and prioritize a broad range of domains relevant to genomics research and public health. The PhenX Steering Committee (SC), chaired by Dr. Jonathan Haines, provides leadership in the selection of domains and domain experts. Members of the SC include outstanding scientists from the research community and liaisons from the Institutes and Centers of the National Institutes of Health. Consensus measures for GWAS will have a direct impact on biomedical research and ultimately on public health. During the course of this project, up to 20 research domains will be examined, with up to 15 measures being recommended for use in future GWAS and other large-scale genomic research efforts. The goal is to maximize the benefits of future research by having comparable measures so that studies can be integrated. Each selected domain will be reviewed by a Working Group (WG) of scientists who are experts in the research area. A systematic review of the literature will guide the WGs selection of up to 15 high priority measures with standardized approaches for measurement. Selection criteria for the measures include factors such as validity, reproducibility, cost, feasibility, and burden to both investigators and participants. The scientific community will be asked to provide input on proposed measures. Consensus development is a key component of the project. | biomedical, domain, genome, health, phenotype, public, research |
has parent organization: RTI International is parent organization of: Phenotypes and eXposures Toolkit is parent organization of: PhenX Phenotypic Terms has organization facet: Phenotypes and eXposures Toolkit |
NHGRI U01 HG004597 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-32816 | SCR_006688 | PhenX - consensus measures for Phenotypes and eXposures, Consensus Measures for Phenotypes Exposures, PhenX (consensus measures for Phenotypes and eXposures), Consensus Measures for Phenotypes Exposure, Consensus Measures for Phenotypes and Exposures | 2026-08-01 12:03:17 | 1 | ||||||
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zfishbook Resource Report Resource Website 1+ mentions |
zfishbook (RRID:SCR_006896) | zfishbook | biomaterial supply resource, material resource | Collection of revertible protein trap gene-breaking transposon (GBT) insertional mutants in zebrafish with active or cryopreserved lines from initially identified lines. Open to community-wide contributions including expression and functional annotation and represents world-wide central hub for information on how to obtain these lines from diverse members of International Zebrafish Protein Trap Consortium (IZPTC) and integration within other zebrafish community databases including Zebrafish Information Network (ZFIN), Ensembl and National Center for Biotechnology Information. Registration allows users to save their favorite lines for easy access, request lines from Mayo Clinic catalog, contribute to line annotation with appropriate credit, and puts them on optional mailing list for future zfishbook newletters and updates. | gene-breaking transposon, expression-tagged, revertible mutation, gene, transposon, mutation, mutant, brain, muscle, skin, secretory, cardiac, brain line, muscle line, skin line, secretory line, cardiac line, plasmid, expression, functional annotation, gene-breaking transposon line, gene-break transposon mutagenesis, cell line, annotation, embryonic zebrafish, larval zebrafish, bio.tools |
is listed by: One Mind Biospecimen Bank Listing is listed by: Debian is listed by: bio.tools is related to: Addgene is related to: Zebrafish International Resource Center has parent organization: Mayo Clinic Minnesota; Minnesota; USA |
Mayo Clinic Cancer Center ; Mayo Foundation ; NIGMS GM63904; NIDA DA14546; NHGRI HG006431 |
PMID:22067444 | Free, Freely available | biotools:zfishbook, nlx_151613 | https://bio.tools/zfishbook | SCR_006896 | book, z fish book, zfishbook, fish, z | 2026-08-01 12:10:39 | 4 | ||||
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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 | 2026-08-02 09:07:16 | 51 | |||||
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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 | 2026-08-02 09:08:13 | 19 | ||||||||
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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 | 2026-08-02 09:08:46 | 8 |
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