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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ChIP-seq Resource Report Resource Website 5000+ mentions |
ChIP-seq (RRID:SCR_001237) | ChIP-seq | data analysis software, data processing software, software application, software resource, software toolkit | Set of software modules for performing common ChIP-seq data analysis tasks across the whole genome, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. The tools are designed to be simple, fast and highly modular. Each program carries out a well-defined data processing procedure that can potentially fit into a pipeline framework. ChIP-Seq is also freely available on a Web interface. | high-throughput sequencing, chromatin immuno precipitation, chip-seq, genome, c |
is listed by: OMICtools has parent organization: SourceForge has parent organization: Ecole Polytechnique Federale de Lausanne; Lausanne; Switzerland has parent organization: SIB Swiss Institute of Bioinformatics |
PMID:27863463 | Free, Available for download, Freely available | OMICS_02103 | https://epd.expasy.org/chipseq/, https://chip-seq.sourceforge.net/ | SCR_001237 | ChIP-seq - Tools for the analysis of ChIP-seq data | 2026-09-19 12:49:38 | 8035 | |||||
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Patchwork Resource Report Resource Website 10+ mentions |
Patchwork (RRID:SCR_000072) | Patchwork | software resource | Software tool for analyzing and visualizing allele-specific copy numbers and loss-of-heterozygosity in cancer genomes. The data input is in the format of whole-genome sequencing data which enables characterization of genomic alterations ranging in size from point mutations to entire chromosomes. High quality results are obtained even if samples have low coverage, ~4x, low tumor cell content or are aneuploid. Patchwork takes BAM files as input whereas PatchworkCG takes input from CompleteGenomics files. TAPS performs the same analysis as Patchwork but for microarray data. | genome, allele, copy number, bam, unix, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Uppsala University; Uppsala; Sweden |
Cancer, Tumor | PMID:23531354 | Free, Available for download, Freely available | biotools:patchwork, OMICS_02118 | https://bio.tools/patchwork | SCR_000072 | 2026-09-19 12:49:15 | 10 | |||||
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Cistrome Resource Report Resource Website 10+ mentions |
Cistrome (RRID:SCR_000242) | data access protocol, software resource, web service | Web based integrative platform for transcriptional regulation studies. | Transcriptional, regulation, Chip, data, analysis, genome, gene, expression, motif, mining, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Galaxy has parent organization: Harvard University; Cambridge; United States |
Dana-Farber Cancer Institute High Tech and Campaign Technology Fund ; National Basic Research Program of China ; NHGRI HG004069; NIDDK DK062434; NIDDK DK074967 |
PMID:21859476 | Free, Freely available | SCR_017663, biotools:cistrome, OMICS_02173 | http://cistrome.org/ap/root, https://bio.tools/cistrome | SCR_000242 | Galaxy Cistrome | 2026-09-19 12:49:18 | 17 | |||||
|
UnSplicer Resource Report Resource Website 1+ mentions |
UnSplicer (RRID:SCR_000226) | software resource | An RNA-seq alignment program that provides alignment of short reads to a reference genome. The program requires two inputs that are provided by the output of GeneMark-ES: HMM model parameters and ab initio gene predictions. UnSplicer is a sister pipeline to TrueSight. | RNA, sequencing, alignment, short reads, genome, genemark-es, gene prediction |
is listed by: OMICtools has parent organization: Georgia Institute of Technology; Georgia; USA |
PMID:24259430 | Free, Available for download, Freely available | OMICS_01806 | SCR_000226 | 2026-09-19 12:49:18 | 1 | ||||||||
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ChromasPro Resource Report Resource Website 10+ mentions |
ChromasPro (RRID:SCR_000229) | data acquisition software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31,2023. Software which is able to assemble data from 454 and Illumina next-generation sequencers, with up to 100,000 sequences if 2 Gb RAM is available. | genome, sequence, dna, assemble, data, illumina, next gen sequence, next generation | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01808 | SCR_000229 | 2026-09-19 12:49:18 | 14 | ||||||||||
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PolyPhen: Polymorphism Phenotyping Resource Report Resource Website 1000+ mentions |
PolyPhen: Polymorphism Phenotyping (RRID:SCR_013189) | PolyPhen, PolyPhen-2, POLYPHEN | data analysis software, data processing software, simulation software, software application, software resource | Software tool which predicts possible impact of amino acid substitution on structure and function of human protein using straightforward physical and comparative considerations. PolyPhen-2 is new development of PolyPhen tool for annotating coding nonsynonymous SNPs. | annotate, nonsynonymous, SNP, predict, coding, damaging, effect, missense, mutation, sequence, variant, phenotype, genetic, disease, exon, protein, coding, fraction, genome, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is related to: OMICtools has parent organization: Harvard University; Cambridge; United States |
PMID:20354512 PMID:23315928 |
SCR_013200, OMICS_00136, nlx_154540, nif-0000-21329, biotools:polyphen, SCR_013238 | https://bio.tools/polyphen | http://www.bork.embl-heidelberg.de/PolyPhen/ | SCR_013189 | PolyPhen, POLYPHEN, PolyPhen-2, Polymorphism Phenotyping, Polymorphism Phenotyping v2 | 2026-09-19 12:52:39 | 4723 | |||||
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eQTL Visualization Tool Resource Report Resource Website 1+ mentions |
eQTL Visualization Tool (RRID:SCR_013413) | data processing software, data visualization software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. eQTL Explorer was developed as a computational resource to visualize and explore data from combined genome-wide expression and linkage studies is essential for the development of testable hypotheses. This visualization tool stores expression profiles, linkage data and information from external sources in a relational database and enables simultaneous visualization and intuitive interpretation of the combined data via a Java graphical interface. eQTL Explorer also provides a new and powerful tool to interrogate these very large and complex datasets. eQTLexplorer allows users to mine and understand data from a repository of genetical genomics experiments. It will graphically display eQTL information based on a certain number of selection criteria, including: tissue type, p-value, cis/trans, probeset Affymetrix id and PQTL type. Sponsors: This work was funded by the MRC Clinical Sciences Centre and the Wellcome Trust programme for Cardiovascular Functional Genomics. | experiment, explore, expression, genome, genetic, genetical, cis, computational, data, database, genomic, grafical, interface, linkage, mine, pqtl type, p-value, repository, tissue, tissue type, trans, visualization, visualize | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10222 | SCR_013413 | eQTLexplorer | 2026-09-19 12:52:42 | 1 | |||||||||
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DOLOP: A Database of Bacterial Lipoproteins Resource Report Resource Website 10+ mentions |
DOLOP: A Database of Bacterial Lipoproteins (RRID:SCR_013487) | data or information resource, data repository, database, service resource, storage service resource | DOLOP is an exclusive knowledge base for bacterial lipoproteins by processing information from 510 entries to provide a list of 199 distinct lipoproteins with relevant links to molecular details. Features include functional classification, predictive algorithm for query sequences, primary sequence analysis and lists of predicted lipoproteins from 43 completed bacterial genomes along with interactive information exchange facility. This website along will have additional information on the biosynthetic pathway, supplementary material and other related figures. DOLOP also contains information and links to molecular details for about 278 distinct lipoproteins and predicted lipoproteins from 234 completely sequenced bacterial genomes. Additionally, the website features a tool that applies a predictive algorithm to identify the presence or absence of the lipoprotein signal sequence in a user-given sequence. The experimentally verified lipoproteins have been classified into different functional classes and more importantly functional domain assignments using hidden Markov models from the SUPERFAMILY database that have been provided for the predicted lipoproteins. Other features include: primary sequence analysis, signal sequence analysis, and search facility and information exchange facility to allow researchers to exchange results on newly characterized lipoproteins. | figure, functional, algorithm, analysis, bacterial, biosynthetic, classification, genome, lipid, lipoprotein, modification, molecular, molecule, pathogenesis, predictive, primary, prokaryote, query, sequence, signal | has parent organization: University of Cambridge; Cambridge; United Kingdom | nif-0000-21124 | SCR_013487 | DOLOP | 2026-09-19 12:52:42 | 16 | |||||||||
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MED Resource Report Resource Website 1+ mentions |
MED (RRID:SCR_013403) | MED | software resource | A non-supervised gene prediction algorithm for prokaryotic genomes with multivariate entropy distance method. | prokaryotic, genome, multivariate entropy distance | is listed by: OMICtools | PMID:17367537 | OMICS_01489 | SCR_013403 | 2026-09-19 12:52:42 | 1 | ||||||||
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Genestack Resource Report Resource Website 1+ mentions |
Genestack (RRID:SCR_011885) | Genestack | service resource | A universal collaborative platform for bioinformatics application development that allows users to store and share large data sets securely within and across organizations, with free access to public data from major databases. The platform includes open-source and proprietary genomics applications, working together independent of file formats. For developers an SDK, APIs and a marketplace are provided. | data sharing, data management, sequencing, quality control, exome, genome, variant call, somatic mutation, rna-seq, chip-seq, data analysis, visualization, computing, big data, next-generation sequencing | is listed by: OMICtools | OMICS_01218 | SCR_011885 | 2026-09-19 12:52:20 | 2 | |||||||||
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Genboree Workbench Resource Report Resource Website |
Genboree Workbench (RRID:SCR_011864) | Genboree | service resource | Service where users are able to upload and store data, access bioinformatics tools, and perform analyses. | metagenome, visualization, genome, transcriptiome, cistrome, epigenome, analysis, rna-seq, chip-seq |
is listed by: OMICtools has parent organization: Baylor University; Texas; USA |
Free for academic use | OMICS_01142 | SCR_011864 | 2026-09-19 12:52:19 | 0 | ||||||||
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Genome Alteration Print Resource Report Resource Website 1+ mentions |
Genome Alteration Print (RRID:SCR_012016) | GAP | software resource | Software for automatic detection of absolute segmental copy numbers and genotype status in complex cancer genome profiles measured by single-nucleotide polymorphism (SNP) arrays. The method is based on pattern recognition of segmented and smoothed copy number and allelic imbalance profiles. The method performs well even for poor-quality data, low tumor content, and highly rearranged tumor genomes. | genome, segmental copy number, genotype, genome profile, copy number, single-nucleotide polymorphism, array |
is listed by: OMICtools has parent organization: Curie Institute; Paris; France |
Cancer, Tumor | PMID:19903341 | OMICS_02119 | SCR_012016 | Genome Alteration Print (GAP): Mining complex cancer genomic profiles | 2026-09-19 12:52:22 | 4 | ||||||
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Human Genome Variation Society Resource Report Resource Website 100+ mentions |
Human Genome Variation Society (RRID:SCR_012989) | HGVS | community building portal, data or information resource, journal article, knowledge environment, meeting resource, portal, training resource | The Society aims to foster discovery and characterization of genomic variations including population distribution and phenotypic associations. We promote collection, documentation and free distribution of genomic variation information and associated clinical variations and endeavor to foster the development of the necessary methodology and informatics. Mission Statement To enhance human health through identification and characterization of changes in the genome that lead to susceptibility to illness. To this end, to collate the genomic information necessary for molecular diagnosis, research on basic mechanisms and design of treatments of human ailments. Society Journal Human Mutation is the Society journal. Members will receive a reduced subscription to the journal if they choose to subscribe. Meetings The Society holds two scientific meetings per year. One as a satellite to either the HUGO (Human Genome Organization) annual meeting or the ESHG (European Society of Human Genetics) annual meeting and one meeting is a satellite to the ASHG (American Society of Human Genetics annual meeting. The meetings are a forum for scientists to exchange ideas and form collaborations. Prominent speakers in the field are invited as well as a call for abstracts at large. The meetings are designed to update and increase knowledge of human genome variation and generally attract a stimulating and interesting collection of abstracts in all fields of human genome variation making it an ideal forum to share information and results. Past themes include: copy number variation, pathogenic or not?, pharmacogenomics, new DNA sequencing technologies, and genotype to pheontype relationships. We invite members and non-members alike to attend these meetings. The Society holds the Annual General Meeting of the members after the scientific meeting that is a satellite of the ASHG. Exhibitor''s booths The Society usually takes out an Exhibitor''s booth at the American & European Societies of Human Genetics annual meetings and sometimes the HUGO HGM meeting. GUIDELINES & RECOMMENDATIONS Members of the Society have formulated Guidelines & Recommendations on a number of topics, but especially for nomenclature of gene variations and guidelines on variation databases. | genetic variation, genome, homo sapiens genome, human, mutation, nomenclature, phenotypic associations, population distribution |
is related to: INFEVERS is parent organization of: HGVS Locus Specific Mutation Databases is parent organization of: Human Genome Variation Society: Databases and Other Tools is parent organization of: Nomenclature for the description of sequence variants is parent organization of: Blood Group Antigen Gene Mutation Database |
nif-0000-23953 | SCR_012989 | 2026-09-19 12:52:36 | 337 | |||||||||
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Genotype-Tissue Expression Resource Report Resource Website 500+ mentions |
Genotype-Tissue Expression (RRID:SCR_013042) | GTEx | biobank, data or information resource, data repository, material storage repository, portal, service resource, storage service resource | Project to study human gene expression and regulation in multiple tissues, providing valuable insights into mechanisms of gene regulation and its disease related perturbations. Genetic variation between individuals will be examined for correlation with differences in gene expression level to identify regions of the genome that influence whether and how much a gene is expressed. Includes initiatives: Novel Statistical Methods for Human Gene Expression Quantitative Trait Loci (eQTL) Analysis ,Laboratory, Data Analysis, and Coordinating Center (LDACC), caHUB Acquisition of Normal Tissues in Support of GTEx Project. | gene expression, regulation, genetic variation, genotype, tissue, tissue bank, database, genome, disease, inherited disease, FASEB list |
is recommended by: National Library of Medicine is listed by: OMICtools |
NIH Common Fund | OMICS_00271 | https://gtexportal.org/home/ | SCR_013042 | GTEx, Genotype-Tissue Expression, Genotype-Tissue Expression (GTEx) | 2026-09-19 12:52:37 | 608 | ||||||
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Human Genome Project Information Resource Report Resource Website 50+ mentions |
Human Genome Project Information (RRID:SCR_013028) | data or information resource, funding resource, narrative resource, portal, slide, topical portal, training material, video resource | This resource gives information about the U.S. Human Genome Project, which was was a 13-year effort to to discover all the estimated 20,000-25,000 human genes and make them accessible for further biological study. The primary project goals were to: - identify all the approximately 20,000-25,000 genes in human DNA, - determine the sequences of the 3 billion chemical base pairs that make up human DNA, - store this information in databases, - improve tools for data analysis, - transfer related technologies to the private sector, and - address the ethical, legal, and social issues (ELSI) that may arise from the project. To help achieve these goals, researchers also studied the genetic makeup of several nonhuman organisms. These include the common human gut bacterium Escherichia coli, the fruit fly, and the laboratory mouse. These parallel studies helped to develop technology and interpret human gene function. Sponsors: The DOE Human Genome Program and the NIH National Human Genome Research Institute (NHGRI) together sponsored the U.S. Human Genome Project. | escherichia coli, fruit fly, function, gene, genome, genetic, bacterium, base pair, biological, dna, human, mouse, sequence, FASEB list |
has parent organization: National Institutes of Health has parent organization: United States Department of Energy |
nif-0000-10252 | SCR_013028 | HGP | 2026-09-19 12:52:37 | 59 | |||||||||
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PhyloPhlAn Resource Report Resource Website 100+ mentions |
PhyloPhlAn (RRID:SCR_013082) | PhyloPhlAn | software resource | Software pipeline for reconstructing highly accurate and resolved phylogenetic trees based on whole-genome sequence information. Pipeline is scalable to thousands of genomes and uses the most conserved 400 proteins for extracting the phylogenetic signal. PhyloPhlAn also implements taxonomic curation, estimation, and insertion operations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | phylogenetic tree, whole-genome sequence, genome, protein |
is listed by: OMICtools is listed by: Debian has parent organization: Harvard T.H. Chan School of Public Health |
PMID:23942190 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01525 | https://sources.debian.org/src/phylophlan/ | SCR_013082 | PhyloPhlAn: microbial Tree of Life using 400 universal proteins | 2026-09-19 12:52:38 | 340 | |||||
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REPCLASS Resource Report Resource Website 10+ mentions |
REPCLASS (RRID:SCR_014654) | data analysis software, data processing software, sequence analysis software, software application, software resource | Tool for the classification of known transposable elements in eukaryotic genomes. It can be combined with ab initio repeat finding in order to recover contrasting transposable element landscapes between species. | transposable element, eukaryotic genome, eukaryote, genome, ab initio, repeat, software, source code, sequence analysis software, data analysis software | DOI:10.1093/gbe/evp023 | Available for download | SCR_014654 | 2026-09-19 12:53:00 | 10 | ||||||||||
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GEMINI Resource Report Resource Website 500+ mentions |
GEMINI (RRID:SCR_014819) | software resource | Framework for exploring genetic variation in the context of the genome annotations available for the human genome. Users can load a VCF file into a database and each variant is automatically annotated by comparing it to several genome annotations from source such as ENCODE tracks, UCSC tracks, OMIM, dbSNP, KEGG, and HPRD. | framework, genetic variation, annotation, human, genome, vcf, database, , bio.tools, FASEB list |
uses: KEGG uses: ENCODE uses: OMIM uses: dbSNP uses: HPRD - Human Protein Reference Database is listed by: Debian is listed by: bio.tools has parent organization: University of Utah; Utah; USA |
DOI:10.1371/journal.pcbi.1003153 | Freely available | biotools:gemini | https://github.com/arq5x/gemini, https://bio.tools/gemini | SCR_014819 | GEnome MINIng (GEMINI), GEMINI - a flexible framework for exploring genome variation, Genome Mining, GEnome MINIng | 2026-09-19 12:53:02 | 532 | ||||||
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CHiCAGO Resource Report Resource Website 100+ mentions |
CHiCAGO (RRID:SCR_014941) | data analysis software, data processing software, software application, software resource, software toolkit | Statistical pipeline for detecting significant chromosomal interactions in Capture Hi-C data. CHiCAGO uses a convolution background model accounting for both random Brownian collisions between chromatin fragments and technical noise. CHiCAGO then performs a p-value weighting procedure based on the expected true positive rates at different distance ranges, with scores representing soft-thresholded -log weighted p-values., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | capture hi-c, capture hi-c data, chic, brownian collisions, chromatin, p-value weighting, genomic organization, genome, statistical analysis, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Babraham Institute |
BBSRC ; MRC UK ; EMBL |
PMID:27306882 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:chicago | https://bitbucket.org/chicagoTeam/chicago, https://bio.tools/chicago | SCR_014941 | Capture HiC Analysis of Genomic Organisation, Capture HiC Analysis of Genomic Organization, CHiCAGO: Capture HiC Analysis of Genomic Organisation | 2026-09-19 12:53:04 | 163 | |||||
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MachiBase Resource Report Resource Website 1+ mentions |
MachiBase (RRID:SCR_003078) | MachiBase | data or information resource, database | Database for Drosophila melanogaster transcription profiling that allows users to search the Drosophilia genome, see sequence overviews, and look at various transcripts. The data were generated in conjunction with the recently developed high-throughput genome sequencer Illumina / Solexa using a newly developed 5'-end mRNA collection method. Approximately 25 million 25-27 nucleotide (nt) 5'-end mRNA tags from the embryos, larvae, young males, young females, old males, old females, and S2 (culture cell line) of D. melanogaster were collected. By arranging this vast amount of expression tag with other annotated data, they have built a one-stop service for Drosophila melanogaster transcription profiling. | transcription profiling, genome, sequence, transcript, mrna, promoter, gene expression, development, embryo, larvae, young, male, female, old, s2, culture, cell line, expressed sequence tag, solexa |
is listed by: OMICtools has parent organization: University of Tokyo; Tokyo; Japan |
PMID:18842623 | Free, Available for download, Freely available | OMICS_01878, nif-0000-03092 | SCR_003078 | 2026-09-19 12:56:38 | 1 |
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