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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Cinteny Resource Report Resource Website 10+ mentions |
Cinteny (RRID:SCR_002147) | software resource, data or information resource, web application, database | Online database for finding and analyzing syntenic regions across multiple genomes and measuring the extent of genome rearrangement using reversal distance as a measure. | syntenic genes, genome rearrangement, online genome database | is listed by: OMICtools | NIAID R21 AI055338; NIAMS R01 AR050688 |
PMID:17343765 | Free, Freely available | OMICS_00931 | SCR_002147 | Cinteny Server for Synteny Identification and Analysis of Genome Rearrangement | 2026-08-05 10:43:34 | 17 | ||||||
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SNP Function Portal Resource Report Resource Website 1+ mentions |
SNP Function Portal (RRID:SCR_001954) | SNP Function Portal | data or information resource, database, data analysis service, production service resource, service resource, analysis service resource | Database for exploring the function implication of single nucleotide polymorphism (SNP) alleles. It is designed to be a clearing house for all public domain SNP functional annotation data, as well as in-house functional annotations derived from different data sources. It currently contains SNP functional annotations in six major categories including genomic elements, transcription regulation, protein function, pathway, disease and population genetics. Besides extensive SNP functional annotations, it includes a search engine that accepts different types of genetic markers as input and identifies all genetically related SNPs based on the HapMap Phase II data as well as the relationship of different markers to known genes. As a result, the system allows users to identify the potential biological impact of genetic markers and complex relationships among genetic markers and genes, and it greatly facilitates knowledge discovery in genome-wide SNP scanning experiments. | single nucleotide polymorphism, linkage disequibrilium, functional annotation, function, annotation, genomic element, transcription regulation, protein function, pathway, disease, population genetics |
is listed by: OMICtools has parent organization: University of Michigan; Ann Arbor; USA |
PMID:16873516 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01928 | SCR_001954 | 2026-08-05 10:43:30 | 4 | |||||||
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SHORTY Resource Report Resource Website 1+ mentions |
SHORTY (RRID:SCR_002048) | data processing software, software application, sequence analysis software, data analysis software, software resource | Software for targeted de novo assembly of microreads with mate pair information and sequencing errors. | sequencing, dna, de novo, microreads, assembler, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:19208115 | Free, Available for download, Freely available | biotools:shorty, OMICS_00030 | https://bio.tools/shorty | SCR_002048 | 2026-08-05 10:43:33 | 3 | |||||||
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NormaCurve Resource Report Resource Website 1+ mentions |
NormaCurve (RRID:SCR_001995) | software resource, data processing software, software application, data analysis software | Analysis methodology that allows simultaneous quantification and normalization of reverse phase protein array (RPPA) data. | analysis, software, code, protein array, RPPA, reverse phase protein array, supplementary material |
is listed by: OMICtools has parent organization: Curie Institute; Paris; France |
PMID:22761696 | Free, Available for download, Freely available | OMICS_00814 | SCR_001995 | 2026-08-05 10:43:31 | 9 | ||||||||
|
SAMTOOLS Resource Report Resource Website 10000+ mentions |
SAMTOOLS (RRID:SCR_002105) | SAMtools | data processing software, software application, data analysis software, sequence analysis software, software toolkit, software resource | Original SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data. | Samtools, BCFtools, HTSlib, next generation sequencing, nucleotide alignments, sequence variant, genomic, c, perl, read, alignment, nucleotide, sequence, data, process, sam, bam, cram, vcf, bcf, bio.tools |
is used by: deFuse is used by: Short Read Sequence Typing for Bacterial Pathogens is used by: ROSE is used by: Fcirc is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: SNVer is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Platypus is related to: shovill is related to: pysam has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom is parent organization of: SAMtools/BCFtools is required by: RelocaTE is required by: Wessim is required by: SL-quant is required by: smMIPfil |
Wellcome Trust ; NHGRI U54 HG002750 |
PMID:19505943 PMID:21903627 DOI:10.1093/bioinformatics/btp352 |
Free, Available for download, Freely available | SCR_018682, biotools:samtools, OMICS_01074, nlx_154607, OMICS_00090 | https://github.com/samtools/samtools, https://github.com/samtools/htslib, https://bio.tools/samtools, https://sources.debian.org/src/samtools/ | http://samtools.sourceforge.net/ | SCR_002105 | samtools, Samtools, Sequence Alignment Map TOOLS, SAMtools, SAM tools | 2026-08-05 10:43:33 | 30156 | |||
|
Cancer Genomics Consortium Resource Report Resource Website 1+ mentions |
Cancer Genomics Consortium (RRID:SCR_002384) | CGC | community building portal, data or information resource, portal, organization portal | Consortium promoting communication and collaboration among cancer cytogenomics laboratories, who are interested in applying microarray technologies to cancer diagnosis and cancer research. Their oals are to (1) establish platform-neutral and cancer specific microarray designs for diagnostic purposes, (2) share cancer microarray data between participating institutions for education purposes, (3) create a public cancer array database, and (4) carry out multicenter cancer genome translational research. Collaboration amongst the different laboratories and researchers will not only provide validation for the microarray design(s) but ultimately provide more comprehensive molecular information and more accurate interpretation to better serve cancer patients and further cancer research. The CGC was officially incorporated in June 2010 as a not-for-profit organization. | cytogenetics, molecular genetics, molecular pathology, microarray technology, cancer diagnosis, cancer research, microarry, cytogenomics, cancer cytogenomics, cancer genetics, genetics | is listed by: OMICtools | Cancer | Membership fee, Account required | OMICS_01776 | SCR_002384 | CCMC, Cancer Cytogenomics Microarray Consortium | 2026-08-05 10:43:36 | 5 | ||||||
|
Clinical and Laboratory Standards Institute Resource Report Resource Website 100+ mentions |
Clinical and Laboratory Standards Institute (RRID:SCR_002382) | CLSI | data or information resource, standard specification, knowledge environment, narrative resource | A not-for-profit membership organization that brings together the global laboratory community to foster excellence in laboratory medicine by facilitating the development of clinical laboratory testing standards based on input from and consensus among industry, government, and health care professionals. CLSI is setting the standard for quality in clinical laboratory testing around the world. | clinical, laboratory testing, quality, clinical laboratory testing standard, laboratory, testing | is listed by: OMICtools | Membership fee | OMICS_01777 | SCR_002382 | 2026-08-05 10:43:38 | 129 | ||||||||
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Quick-R Resource Report Resource Website 1+ mentions |
Quick-R (RRID:SCR_002417) | Quick-R | book, data or information resource, training material, narrative resource | Training material created for both current R users, and experienced users of other statistical packages (e.g., SAS, SPSS, Stata) who would like to transition to R to help you quickly access this language in your work. The book inspired by this site takes the material here and significantly expands upon it. | r, programming language, code | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_01760 | SCR_002417 | Quick-R - accessing the power of R | 2026-08-05 10:43:37 | 4 | |||||||
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realSFS Resource Report Resource Website 10+ mentions |
realSFS (RRID:SCR_002493) | software resource, data processing software, software application, data analysis software | Software program used to estimate allele frequency and SNP calling., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | allele frequency estimation, snp calling | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00071 | SCR_002493 | 2026-08-05 10:43:39 | 26 | |||||||||
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R Tutorial - An R Introduction to Statistics Resource Report Resource Website 10+ mentions |
R Tutorial - An R Introduction to Statistics (RRID:SCR_002394) | R Tutorial | book, data or information resource, training material, narrative resource | Couple of introductory tutorials on basic R concepts that provides an introduction to the R programming language, and illustrates its use by solving elementary statistics textbook exercises. Beyond the basics, they also cover topics of GPU computing in R. An R Tutorial eBook is also available. | r, statistics, gpu computing | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_01762 | SCR_002394 | R Tutorial (An R Introduction to Statistics) | 2026-08-05 10:43:36 | 21 | |||||||
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CTCFBSDB Resource Report Resource Website 50+ mentions |
CTCFBSDB (RRID:SCR_002279) | CTCFBSDB, CTCFBSDB 2.0 | data or information resource, database, data analysis service, production service resource, service resource, analysis service resource |
A comprehensive collection of experimentally determined and computationally predicted CCCTC-binding factor (CTCF) binding sites (CTCFBS) from the literature. The database is designed to facilitate the studies on insulators and their roles in demarcating functional genomic domains. The CTCFBS Prediction Tool allows users to scan sequences for the single best match to CTCF position weight matrices. Currently (March 2014), the database contains almost 15 million experimentally determined CTCF binding sites across several species. CTCF binding sites were collected from published papers containing CTCF binding sites identified using ChIPSeq or similar methods, data from the ENCODE project, and a set of approximately 100 manually curated binding sites identified by low-throughput experiments. Users can browse insulator sequence features, function annotations, genomic contexts including histone methylation profiles, flanking gene expression patterns and orthologous regions in other mammalian genomes. Users can also retrieve data by text search, sequence search and genomic range search. |
cctc-binding factor, ctcf, ctcf binding site, insulator, genomic insulator, genome, binding site, FASEB list |
is listed by: OMICtools has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
PMID:23193294 PMID:17981843 |
nif-0000-02703, OMICS_00530 | http://insulatordb.utmem.edu/ | SCR_002279 | CTCFBSDB: a CTCF binding site database for characterization of vertebrate genomic insulators, CTCFBSDB 2.0: A database for CTCF binding sites and genome organization | 2026-08-05 10:43:36 | 63 | ||||||
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Variant Reporter Software Resource Report Resource Website 50+ mentions |
Variant Reporter Software (RRID:SCR_002329) | data processing software, software application, sequence analysis software, data analysis software, software resource |
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 28, 2017. Software that performs comparative sequencing, also known as direct sequencing, medical sequencing, PCR sequencing and resequencing with DNA sequencing files. The software is designed for reference based and non-reference based analysis such as mutation detection and analysis, SNP discovery and validation and sequence confirmation. |
comparative sequencing, mutation detection, snp discovery, sequence confirmation |
is listed by: OMICtools is listed by: Thermo Fisher Scientific has parent organization: Life Technologies |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01818 | http://www.lifetechnologies.com/order/catalog/product/4385261 | SCR_002329 | 2026-08-05 10:43:38 | 85 | ||||||||
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DNA DataBank of Japan (DDBJ) Resource Report Resource Website 500+ mentions |
DNA DataBank of Japan (DDBJ) (RRID:SCR_002359) | DDBJ | data or information resource, data repository, database, storage service resource, service resource | Maintains and provides archival, retrieval and analytical resources for biological information. Central DDBJ resource consists of public, open-access nucleotide sequence databases including raw sequence reads, assembly information and functional annotation. Database content is exchanged with EBI and NCBI within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). In 2011, DDBJ launched two new resources: DDBJ Omics Archive and BioProject. DOR is archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between the ArrayExpress at EBI and DOR in the common MAGE-TAB format. BioProject provides organizational framework to access metadata about research projects and data from projects that are deposited into different databases. | nucleotide sequence, genome, dna, dna database, dna research, nucleotide, phylogenetics, protein, sequence, protein binding, gene expression, gene, genetics, nucleoid, genomics, protein binding, gold standard, bio.tools, FASEB list |
is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: re3data.org is listed by: Debian is listed by: bio.tools is related to: INSDC is related to: GenBank is related to: INSDC is related to: European Nucleotide Archive (ENA) is related to: GenBank is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: Worldwide Protein Data Bank (wwPDB) is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: PDBe - Protein Data Bank in Europe is related to: PDBe - Protein Data Bank in Europe is related to: European Nucleotide Archive (ENA) is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: NCBI Assembly Archive Viewer has parent organization: National Institute of Genetics; Shizuoka; Japan is parent organization of: DDBJ Omics Archive is parent organization of: BodyMap-Xs is parent organization of: DDBJ Sequence Read Archive is parent organization of: CIBEX: Center for Information Biology gene EXpression database is parent organization of: Japanese Genotype-phenotype Archive (JGA) |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:26578571 PMID:25477381 |
Free, Freely available, | OMICS_01644, biotools:ddbj, nif-0000-02740, r3d100010218 | https://bio.tools/ddbj, https://doi.org/10.17616/R3M01R | SCR_002359 | DNA DataBank of Japan (DDBJ), DNA DataBank of Japan, DDBJ, DNA Data Bank of Japan, DDBJ - DNA Data Bank of Japan | 2026-08-05 10:43:38 | 627 | ||||
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Mason Resource Report Resource Website 100+ mentions |
Mason (RRID:SCR_002476) | software application, simulation software, software resource | Collection of software tools for simulating biological sequences, including simulations of genome fragment sampling, random genomic sequences, methylation levels, and NGS reads. | read simulating software, sequencing simulation, haplotype simulation | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_00252 | SCR_002476 | Mason2 | 2026-08-05 10:43:39 | 164 | ||||||||
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PILER Resource Report Resource Website 10+ mentions |
PILER (RRID:SCR_017333) | software resource, data processing software, software application, data analysis software | Software tool for analyzing repetitive DNA found in genome sequences. Software package for identification and classification of genomic repeats. Used for identifying patterns of local alignments induced by certain classes of repeats. | analysis, repetitive, DNA, genome, sequence, classification, alignment | is listed by: OMICtools | PMID:15961452 | Free, Available for download, Freely available | https://omictools.com/piler-tool | SCR_017333 | 2026-08-05 10:46:53 | 15 | ||||||||
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Phangorn Resource Report Resource Website 10+ mentions |
Phangorn (RRID:SCR_017302) | data processing software, software application, data visualization software, data analysis software, software toolkit, software resource | Software R package for phylogenetic reconstruction and analysis. Used for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation. Allows to compare trees, models selection and offers visualizations for trees and split networks. | phylogenetic, tree, network, reconstruction, analysis, estimation, Maximum, Likelihood, Parsimony, distance, method, Hadamard conjugation |
is listed by: Debian is listed by: OMICtools is related to: CRAN |
Muséum National D Histoire Naturelle | DOI:10.1093/bioinformatics/btq706 | Free, Available for download, Freely available | OMICS_12497 | https://github.com/KlausVigo/phangorn, https://sources.debian.org/src/r-cran-phangorn/ | SCR_017302 | Phangorn R package | 2026-08-05 10:46:45 | 24 | |||||
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BioAssay Express Resource Report Resource Website |
BioAssay Express (RRID:SCR_017594) | data access protocol, service resource, software resource, web service | Web based tool for annotating bioassay protocols using semantic web terms. Enables searching, sorting, clustering and analyzing of assays without needing to read through original text. Exploits Common Assay Template based on underlying vocabularies and semantic standards from BioAssay Ontology, Drug Target Ontology, Cell Line Ontology and others. Users can identify similar assays and examine similarity of assays between and within organizations. | Annotating, bioassay, protocol, semantic, web, term, ontology | is listed by: OMICtools | NCATS R44 TR000185 | DOI:10.7717/peerj-cs.61 | Free, Freely available | https://github.com/cdd/bioassay-template | SCR_017594 | 2026-08-05 10:46:55 | 0 | |||||||
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GADMA Resource Report Resource Website 1+ mentions |
GADMA (RRID:SCR_017680) | GADMA | software resource, data processing software, software application, data analysis software | Software tool to implement methods for automatic inferring joint demographic history of multiple populations from genetic data. Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data. | Inferring, demographic, history, population, genetic, data, allele, frequency, spectrum, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1101/407734 | Free, Available for download, Freely available | biotools:GADMA | https://bio.tools/GADMA | SCR_017680 | Genetic Algorithm for Demographic Model Analysis | 2026-08-05 10:46:56 | 3 | |||||
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GeneATLAS Resource Report Resource Website 100+ mentions |
GeneATLAS (RRID:SCR_017577) | data or information resource, database, atlas, data analysis service, production service resource, service resource, analysis service resource | Database of associations between traits and variants using UK Biobank cohort. Searchable atlas of genetic associations. Assists researchers to query UK Biobank. Provides unbiased view of phenotype and genotype associations across of traits. | Association, trait, variant, UK Biobank, cohort, atlas, genetic, phenotype, genotype, FASEB list |
is listed by: OMICtools has parent organization: University of Edinburgh; Scotland; United Kingdom |
Free, Available for download, Freely available | SCR_017577 | Gene ATLAS, Gene Atlas | 2026-08-05 10:46:55 | 132 | |||||||||
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immuneXpresso Resource Report Resource Website |
immuneXpresso (RRID:SCR_017578) | data or information resource, software application, software resource, service resource, text-mining software | Software tool as text-mining engine that structures and standardizes knowledge of immune intercellular communication. Knowledgebase contains interactions and separate mentions of cells or cytokines in context of thousands of diseases. Intercellular interactions were text-mined from all available PubMed abstracts across disease conditions. | Structure, standardize, immune, cellular, interaction, cytokine, disease, cell, PubMed, abstract |
is listed by: NIDDK Information Network (dkNET) is listed by: OMICtools |
NIH ; NIAID ; Rappaport Family Institute for Research in the Medical Sciences |
PMID:29912209 | Free, Freely available | SCR_017578 | 2026-08-05 10:46:49 | 0 |
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