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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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LRPath Resource Report Resource Website 1+ mentions |
LRPath (RRID:SCR_018572) | analysis service resource, web service, software resource, data access protocol, production service resource, service resource | Web tool to perform gene set enrichment testing. Used to test for predefined biologically relevant gene sets that contain more significant genes from experimental dataset than expected by chance. Logistic regression approach for identifying enriched biological groups in gene expression data. | Gene, map, gene set, gene set testing, identifying enriched biologically group, gene expression data, gene expression, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
NIEHS P30 ES06096; NIEHS U01 ES015675; NHGRI R01 HG003749; NLM R01 LM008106; NIDA U54 DA021519 |
PMID:19038984 | Free, Freely available | biotools:lrpath | https://bio.tools/lrpath | SCR_018572 | 2026-08-04 09:44:25 | 4 | ||||||
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Mash Resource Report Resource Website 50+ mentions |
Mash (RRID:SCR_019135) | software application, software resource, data analytics software | 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 | 2026-08-04 09:44:32 | 54 | ||||||
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CHISEL Resource Report Resource Website 1+ mentions |
CHISEL (RRID:SCR_023220) | CHISEL | software application, software resource | Software tool to infer allele and haplotype specific copy numbers in individual cells from low coverage single cell DNA sequencing data. Integrates weak allelic signals across individual cells, powering strength of single cell sequencing technologies to overcome weakness. Includes global clustering of RDRs and BAFs, and rigorous model selection procedure for inferring genome ploidy that improves both inference of allele specific and total copy numbers. | infer allele and haplotype specific copy numbers, individual cells, low coverage single cell DNA sequencing data, weak allelic signals, weak signals integration, | NHGRI R01HG007069; NCI U24CA211000; NSF CCF 1053753; Chan Zuckerberg Initiative DAF grants ; NCI P30CA072720; O’Brien Family Fund for Health Research ; Wilke Family Fund for Innovation |
DOI:10.1038/s41587-020-0661-6 | Free, Available for download, Freely available | SCR_023220 | Copy-number Haplotype Inference in Single-cell by Evolutionary Links | 2026-08-04 09:45:13 | 2 | |||||||
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HaploReg Resource Report Resource Website 1000+ mentions |
HaploReg (RRID:SCR_006796) | HaploReg | database, data or information resource | HaploReg is a tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Using linkage disequilibrium (LD) information from the 1000 Genomes Project, linked SNPs and small indels can be visualized along with their predicted chromatin state in nine cell types, conservation across mammals, and their effect on regulatory motifs. HaploReg is designed for researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation. | chromatin state, conservation, regulatory motif, alteration, variant, chromatin, motif, annotation, genome, variation, genome-wide association study, refsnp, refseq gene, snp, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Broad Institute |
NHGRI R01-HG004037; NHGRI RC1-HG005334; NSF 0644282 |
PMID:22064851 | biotools:HaploReg, nlx_151407 | http://compbio.mit.edu/HaploReg, https://bio.tools/HaploReg | SCR_006796 | 2026-08-04 09:41:42 | 1004 | ||||||
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Public Expression Profiling Resource Resource Report Resource Website 10+ mentions |
Public Expression Profiling Resource (RRID:SCR_007274) | PEPR | database, data or information resource | An experiment in web-database access to large multi-dimensional data sets using a standardized experimental platform to determine if the larger scientific community can be given simple, intuitive, and user-friendly web-based access to large microarray data sets. All data in PEPR is also available via NCBI GEO. The structure and goals of PEPR differ from other mRNA expression profiling databases in a number of important ways. * The experimental platform in PEPR is standardized, and is an Affymetrix - only database. All microarrays available in the PEPR web database should ascribe to quality control and standard operating procedures. A recent publication has described the QC/SOP criteria utilized in PEPR profiles ( The Tumor Analysis Best Practices Working Group 2004 ). * PEPR permits gene-based queries of large Affymetrix array data sets without any specialized software. For example, a number of large time series projects are available within PEPR, containing 40-60 microarrays, yet these can be simply queried via a dynamic web interface with no prior knowledge of microarray data analysis. * Projects in PEPR originate from scientists world-wide, but all data has been generated by the Research Center for Genetic Medicine, Children''''s National Medical Center, Washington DC. Future developments of PEPR will allow remote entry of Affymetrix data ascribing to the same QC/SOP protocols. They have previously described an initial implementation of PEPR, and a dynamic web-queried time series graphical interface ( Chen et al. 2004 ). A publication showing the utility of PEPR for pharmacodynamic data has recently been published ( Almon et al. 2003 ). | microarray, expression profiling, affymetrix, metadata standard, gene, time series, data sharing, visualization, data mining, platform, blood, cell, cancer, bone, brain, eye, gut, heart, kidney, liver, lung, muscle, spinal cord, spleen, analysis |
is listed by: OMICtools is related to: Gene Expression Omnibus |
NINDS ; United States Department of Defense ; NHGRI ; NHLBI |
PMID:14681485 PMID:14596642 |
Public, Account required, (to download, For the analysis and visualization tools), The community can contribute to this resource | nif-0000-00014, OMICS_00776 | SCR_007274 | 2026-08-04 09:41:48 | 16 | ||||||
|
ESEfinder 3.0 Resource Report Resource Website 100+ mentions |
ESEfinder 3.0 (RRID:SCR_007088) | ESEfinder | data analysis service, analysis service resource, production service resource, service resource | A web-based resource that facilitates rapid analysis of exon sequences to identify putative exonic splicing enhancers (ESEs) responsive to the human SR proteins SF2/ASF, SC35, SRp40 and SRp55, and to predict whether exonic mutations disrupt such elements. | exonic splicing enhancer, sr protein, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Cold Spring Harbor Laboratory |
NIGMS GM42699; NCI CA88351; NHGRI HG01696 |
PMID:12824367 | Free for non-profit use, Non-commercial, Acknowledgement requested, Commercial use with license | biotools:esefinder, nif-0000-30496 | http://rulai.cshl.edu/tools/ESE2/, https://bio.tools/esefinder | http://exon.cshl.edu/ESE/ | SCR_007088 | 2026-08-04 09:41:46 | 211 | ||||
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PEPATAC Resource Report Resource Website 1+ mentions |
PEPATAC (RRID:SCR_024758) | software resource, software toolkit | Software standardized pipeline for ATAC-seq data analysis with serial alignments. Leverages unique features of ATAC-seq data to optimize for speed and accuracy, and provides several unique analytical approaches. Downstream analysis is simplified by standard definition format, modularity of components, and metadata APIs in R and Python. Restartable, fault-tolerant, and can be run on local hardware, using any cluster resource manager, or in provided Linux containers. We also emphasize the advantage of aligning to the mitochondrial genome serially, which improves alignment and quality control metrics. Includes quality control plots, summary statistics, and variety of data formats. | ATAC-seq analysis pipeline, ATAC-seq data, analysis, serial alignments, | NHGRI RM1 HG007735; NIGMS R35 GM128636; Howard Hughes Medical Institute ; American Society of Hematology |
PMID:34859208 | Free, Available for download, Freely available | https://github.com/databio/PEPATAC/releases | SCR_024758 | 2026-08-04 09:45:35 | 2 | ||||||||
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Single Cell Pathway Analysis Resource Report Resource Website 1+ mentions |
Single Cell Pathway Analysis (RRID:SCR_024909) | SCPA | data processing software, source code, data analysis software, software resource, software application | Software R package for pathway analysis in scRNA-seq data. It’s a different approach to pathway analysis that defines pathway activity as a change in multivariate distribution of a given pathway across conditions, rather than enrichment or over representation of genes. | pathway analysis, scRNA-seq data analysis, single cell RNA-seq data, | NHGRI R01 HG006137; Intramural Research Program of the NIH ; National Heart ; Lung ; and Blood Institute |
PMID:36417885 | Free, Available for download, Freely available | https://github.com/jackbibby1/SCPA/ | SCR_024909 | Single Cell Pathway Analysis (SCPA) | 2026-08-04 09:45:38 | 1 | ||||||
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TheCellMap Resource Report Resource Website 10+ mentions |
TheCellMap (RRID:SCR_018728) | database, data or information resource, service resource | 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 | 2026-08-04 09:44:27 | 34 | |||||||
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Dfam Resource Report Resource Website 50+ mentions |
Dfam (RRID:SCR_021168) | database, data or information resource | 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 | 2026-08-04 09:44:44 | 82 | |||||||
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CloVR Resource Report Resource Website 10+ mentions |
CloVR (RRID:SCR_005290) | CloVR | software resource, service resource | A desktop application for push-button automated sequence analysis that can utilize cloud computing resources. CloVR is implemented as a single portable virtual machine (VM) that provides several automated analysis pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis. The CloVR VM runs on a personal computer, utilizes local computer resources and requires minimal installation, addressing key challenges in deploying bioinformatics workflows. In addition CloVR supports use of remote cloud computing resources to improve performance for large-scale sequence processing. | cloud computing, next-generation sequencing |
is listed by: OMICtools has parent organization: University of Maryland; Maryland; USA |
Amazon Web Services in Education Research Grants program ; National Human Genome Research Institute ; NHGRI RC2 HG005597-01; NSF 0949201 |
PMID:21878105 | OMICS_01216 | SCR_005290 | CloVR - Automated Sequence Analysis from Your Desktop, Cloud Virtual Resource | 2026-08-04 09:41:19 | 26 | ||||||
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Mouse Genome Database Resource Report Resource Website 500+ mentions |
Mouse Genome Database (RRID:SCR_012953) | MGD | database, data or information resource | 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 | 2026-08-04 09:43:06 | 502 | |||||
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PhenoDB Resource Report Resource Website 1+ mentions |
PhenoDB (RRID:SCR_016551) | database, data or information resource | 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 | 2026-08-04 09:43:55 | 5 | |||||||
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RegulomeDB Resource Report Resource Website 100+ mentions |
RegulomeDB (RRID:SCR_017905) | database, data or information resource, service resource | 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 | 2026-08-04 09:44:15 | 123 | |||||||||
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HumanBase Resource Report Resource Website 50+ mentions |
HumanBase (RRID:SCR_016145) | database, data or information resource | 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 | 2026-08-04 09:43:50 | 74 | ||||||||
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Open Regulatory Annotation Database Resource Report Resource Website 50+ mentions |
Open Regulatory Annotation Database (RRID:SCR_007835) | ORegAnno | database, data or information resource | Open source, open access database and literature curation system for community based annotation of experimentally identified DNA regulatory regions, transcription factor binding sites and regulatory variants. Automatically cross referenced against PubMED, Entrez Gene, EnsEMBL, dbSNP, eVOC: Cell type ontology, and Taxonomy database. Community driven resource for curated regulatory annotation. | Collection, annotation, curated, experimentally, identified, DNA, regulatory, region, element, transcript, factor, binding, site, regulatory, variant, data, FASEB list |
has parent organization: University of Manchester; Manchester; United Kingdom works with: PubMed works with: Entrez Gene works with: Ensembl works with: dbSNP |
British Columbia Cancer Foundation ; Genome Canada ; Genome British Columbia ; European Network of Excellence ; BioSapiens Network of Excellence ; Research Foundation – Flanders ; Pleiades Promoter Project ; Michael Smith Foundation for Health Research ; Canadian Institutes of Health Research ; European Molecular Biology Laboratory ; Marie Curie Early Stage Research Training Fellowship ; Natural Sciences and Engineering Research Council ; Swedish Research Council ; American Cancer Society ; Edward Mallinckrodt ; Jr. Foundation ; NHGRI K99 HG007940; NHGRI R01 HG008150; NIMH R01 MH101814; NCI K22 CA188163 |
PMID:18006570 PMID:26578589 |
Free, Freely available | nif-0000-03223, r3d100010656 | http://www.oreganno.org/, https://doi.org/10.17616/R3DG70 | SCR_007835 | Open REGulatory ANNOtation, ORegAnno 3.0 | 2026-08-04 09:42:01 | 81 | ||||
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UniRef Resource Report Resource Website 100+ mentions |
UniRef (RRID:SCR_010646) | database, data or information resource | Databases which provide clustered sets of sequences from UniProt Knowledgebase and selected UniParc records, in order to obtain complete coverage of sequence space at several resolutions while hiding redundant sequences from view. The UniRef100 database combines identical sequences and sub-fragments with 11 or more residues (from any organism) into a single UniRef entry. The sequence of a representative protein, the accession numbers of all the merged entries, and links to the corresponding UniProtKB and UniParc records are all displayed in the entry. UniRef90 and UniRef50 are built by clustering UniRef100 sequences with 11 or more residues such that each cluster is composed of sequences that have at least 90% (UniRef90) or 50% (UniRef50) sequence identity to the longest sequence (UniRef seed sequence). All the sequences in each cluster are ranked to facilitate the selection of a representative sequence for the cluster. | database, protein sequence, sub-fragment, sequence cluster, clustered set |
is related to: VIROME is related to: UniRef at the EBI is related to: BioExtract has parent organization: UniProt |
NHGRI U01 HG02712 | PMID:17379688 | Updated biweekly | nlx_66133, r3d100011518 | SCR_010646 | UniProt Reference Clusters | 2026-08-04 09:42:46 | 277 | ||||||
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HiCDCPlus Resource Report Resource Website 1+ mentions |
HiCDCPlus (RRID:SCR_025317) | software resource, software toolkit | Software package for Hi-C/HiChIP interaction calling and differential analysis using efficient implementation of HiC-DC statistical framework. Enables principled statistical analysis of Hi-C and HiChIP data sets. Enables systematic 3D interaction calls and differential analysis for Hi-C and HiChIP | Hi-C/HiChIP interaction calling, differential analysis, statistical analysis of Hi-C and HiChIP data sets, systematic 3D interaction calls, | NHGRI U01 HG009395; NIDDK U01 DK128852 |
PMID:34099725 | Free, Available for download, Freely available | https://bitbucket.org/leslielab/hicdcplus/src/master/ | SCR_025317 | , HiC-DC+, Hi-C Direct Caller Plus, HiCDCPlus (HiC-DC+) | 2026-08-04 09:45:49 | 1 | |||||||
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tRNA Analysis of eXpression Resource Report Resource Website 1+ mentions |
tRNA Analysis of eXpression (RRID:SCR_025486) | tRAX | data processing software, software application, software resource, data analysis software | Software package built for in-depth analyses of tRNA-derived small RNAs (tDRs), mature tRNAs, and inference of RNA modifications from high-throughput small RNA sequencing data. Used for integrating analysis of tRNAs, tRNA-derived small RNAs, and tRNA modifications. | tRNA-derived small RNAs, mature tRNAs, inference of RNA modifications, high-throughput small RNA sequencing data, | has parent organization: University of California at Santa Cruz; California; USA | NHGRI R01HG006753 | DOI:10.1101/2022.07.02.498565 PMID:26214130 |
Free, Available for download, Freely available, | SCR_025486 | tRNA Analysis of eXpression (tRAX) | 2026-08-04 09:45:46 | 3 | ||||||
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glmpca Resource Report Resource Website 1+ mentions |
glmpca (RRID:SCR_025517) | software resource, software toolkit, source code | Software R package for dimension reduction of non-normally distributed data. Generalized PCA for non-normally distributed data. | dimension reduction, non-normally distributed data, principal components analysis, | NCI T32CA009337; NHGRI R00HG009007; Chan-Zuckerberg Initiative ; NHGRI R01HG005220; NIGMS R01GM083084; NHGRI P41HG004059 |
PMID:31870412 | Free, Available for download, Freely available, | https://CRAN.R-project.org/package=glmpca | SCR_025517 | generalized version of principal components analysis | 2026-08-04 09:45:51 | 1 |
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