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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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CLIPZ Resource Report Resource Website 10+ mentions |
CLIPZ (RRID:SCR_005755) | CLIPZ | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 20,2019.Database and analysis environment for experimentally determined binding sites of RNA-binding proteins. It supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins in order to identify the binding sites of these proteins. The functional annotation could be also applied to short reads resulting from other types of experiments such as mRNA-Seq, Digital Gene Expression, small RNA cloning, etc. The platform enables visualization and mining of individual data sets as well as analysis involving multiple experimental data sets. The platform can support collaborative projects involving multiple users and groups of users as well as public and private datasets. | rna-binding protein, binding site, protein, functional annotation, cross-linking and immunoprecipitation, short read, mrna-seq, digital gene expression, small rna cloning, visualization, mining, analysis, post-transcriptional regulatory element, genome, transcript, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SIB Swiss Institute of Bioinformatics has parent organization: University of Basel; Basel; Switzerland |
PMID:21087992 | THIS RESOURCE IS NO LONGER IN SERVICE. | OMICS_02256, biotools:clipz | https://bio.tools/clipz | SCR_005755 | 2026-09-05 06:25:41 | 20 | ||||||
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959 Nematode Genomes Resource Report Resource Website 1+ mentions |
959 Nematode Genomes (RRID:SCR_006068) | NematodeGenomes | data or information resource, narrative resource, wiki | A collaborative wiki that collates information on completed, ongoing and planned genome and transcriptome sequencing projects on species from phylum Nematoda. The intention is to encourage genome sequencing across the diversity of the phylum Nematoda. Wiki includes: * Published complete nematode genomes: A dynamically generated table of all species for which the genome is published. * Nematode species with genomes in progress: A dynamically generated table of all species for which a genome project is underway. Users may add species to the list * Proposed nematode genome projects: To propose a species for genome sequencing, edit its species page, and set the genome project status to proposed. * BLAST server: Search a number of the nematode-genomes-in-progress with genes of your choice. Currently there are 12 draft genomes available... * Genomes with Data available: Genomes with data available for download. Users may add more data URLs to strain pages or update the URLs. | nematode, genome, genome sequencing, transcriptome sequencing, blast, genomics, sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: nematodes.org has parent organization: University of Edinburgh; Scotland; United Kingdom |
NERC | PMID:22058131 | nlx_151473, biotools:959_nematode_genomes | https://bio.tools/959_nematode_genomes | SCR_006068 | NematodeGenomes | 2026-09-05 06:25:46 | 2 | |||||
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OligoGenome Resource Report Resource Website 1+ mentions |
OligoGenome (RRID:SCR_006025) | OligoGenome | data or information resource, database, resource | The Stanford Human OligoGenome Project hosts a database of capture oligonucleotides for conducting high-throughput targeted resequencing of the human genome. This set of capture oligonucleotides covers over 92% of the human genome for build 37 / hg19 and over 99% of the coding regions defined by the Consensus Coding Sequence (CCDS). The capture reaction uses a highly multiplexed approach for selectively circularizing and capturing multiple genomic regions using the in-solution method developed in Natsoulis et al, PLoS One 2011. Combined pools of capture oligonucleotides selectively circularize the genomic DNA target, followed by specific PCR amplification of regions of interest using a universal primer pair common to all of the capture oligonucleotides. Unlike multiplexed PCR methods, selective genomic circularization is capable of efficiently amplifying hundreds of genomic regions simultaneously in multiplex without requiring extensive PCR optimization or producing unwanted side reaction products. Benefits of the selective genomic circularization method are the relative robustness of the technique and low costs of synthesizing standard capture oligonucleotide for selecting genomic targets. | oligonucleotide, genome, probe, coding region, oligonucleotide sequence, chromosome | has parent organization: Stanford University; Stanford; California | NHGRI RC2 HG005570-01; NCI R21CA12848; NCI 5K08CA96879?6; NIDDK DK56339; NHGRI 2P01HG000205; NLM T15-LM007033; Doris Duke Clinical Foundation ; Reddere Foundation ; Liu Bie Ju Cha and Family Fellowship in Cancer ; Wang Family Foundation ; Howard Hughes Medical Foundation |
PMID:22102592 | nlx_151422 | SCR_006025 | Stanford Human Oligo Genome Project, Human OligoGenome Resource, Stanford Human Oligo Genome, Human Oligo Genome, Human OligoGenome | 2026-09-05 06:25:45 | 2 | ||||||
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ICEberg Resource Report Resource Website 50+ mentions |
ICEberg (RRID:SCR_006026) | ICEberg | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | ICEberg is an integrated database that provides comprehensive information about integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome. An ICE contains three typical modules, integration and excision, conjugation, and regulation modules, that collectively promote vertical inheritance and periodic lateral gene flow. Many ICEs carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. ICEberg offers a unique, highly organized, readily explorable archive of both predicted and experimentally supported ICE-relevant data. It currently contains details of 428 ICEs found in representatives of 124 bacterial species, and a collection of >400 directly related references. A broad range of similarity search, sequence alignment, genome context browser, phylogenetic and other functional analysis tools are readily accessible via ICEberg. ICEberg will facilitate efficient, multidisciplinary and innovative exploration of bacterial ICEs and be of particular interest to researchers in the broad fields of prokaryotic evolution, pathogenesis, biotechnology and metabolism. The ICEberg database will be maintained, updated and improved regularly to ensure its ongoing maximum utility to the research community. | dna, protein, sequence, chromosome, element, gene, similarity search, sequence alignment, genome, phylogenetic, functional analysis, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: Shanghai Jiao Tong University; Shanghai; China |
National Natural Science Foundation of China 973 program 2009CB118901; National Natural Science Foundation of China 973 program 2012CB721002; National Natural Science Foundation of China 863 program 2011BAD23B05-3; Ministry of Science and Technology China ; Ministry of Education China NCET-10-0572; Shanghai Jiaotong University ; Shanghai Municipality ; Action Medical Research SP4255; Innovation Fellowship ; East Midlands Development Agency |
PMID:22009673 | nlx_151424, biotools:iceberg | https://bio.tools/iceberg | SCR_006026 | ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria | 2026-09-05 06:25:46 | 89 | |||||
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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 | 2026-09-05 06:24:11 | 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 | 2026-09-05 06:24:15 | 17 | |||||
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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 | 2026-09-05 06:24:14 | 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 | 2026-09-05 06:24:16 | 14 | ||||||||||
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InterPro Resource Report Resource Website 5000+ mentions |
InterPro (RRID:SCR_006695) | InterPro | analysis service resource, data access protocol, data analysis service, data or information resource, database, production service resource, service resource, software resource, web service | Service providing functional analysis of proteins by classifying them into families and predicting domains and important sites. They combine protein signatures from a number of member databases into a single searchable resource, capitalizing on their individual strengths to produce a powerful integrated database and diagnostic tool. This integrated database of predictive protein signatures is used for the classification and automatic annotation of proteins and genomes. InterPro classifies sequences at superfamily, family and subfamily levels, predicting the occurrence of functional domains, repeats and important sites. InterPro adds in-depth annotation, including GO terms, to the protein signatures. You can access the data programmatically, via Web Services. The member databases use a number of approaches: # ProDom: provider of sequence-clusters built from UniProtKB using PSI-BLAST. # PROSITE patterns: provider of simple regular expressions. # PROSITE and HAMAP profiles: provide sequence matrices. # PRINTS provider of fingerprints, which are groups of aligned, un-weighted Position Specific Sequence Matrices (PSSMs). # PANTHER, PIRSF, Pfam, SMART, TIGRFAMs, Gene3D and SUPERFAMILY: are providers of hidden Markov models (HMMs). Your contributions are welcome. You are encouraged to use the ''''Add your annotation'''' button on InterPro entry pages to suggest updated or improved annotation for individual InterPro entries. | protein, classify, prediction, protein domain, genome, protein family, functional site, protein sequence, protein function, analysis, nucleic acid, amino acid, amino acid sequence, gold standard |
is listed by: re3data.org is listed by: OMICtools is related to: TIGRFAMS is related to: TIGRFAMS is related to: FlyMine is related to: GeneSpeed- A Database of Unigene Domain Organization is related to: Biomine is related to: InterProScan is related to: GeneTerm Linker is related to: Gene Ontology is related to: ProDom is related to: Algal Functional Annotation Tool has parent organization: European Bioinformatics Institute |
European Union FP7 Scientific Data Repositories 213037; BBSRC BB/F010508/1; NIGMS GM081084 |
PMID:22096229 PMID:21082426 PMID:18940856 PMID:18428686 PMID:18025686 PMID:17202162 PMID:16909843 PMID:15608177 PMID:12520011 PMID:12230031 PMID:11159333 PMID:11119311 PMID:11125043 |
Acknowledgement requested, Free, Public, The community can contribute to this resource | nif-0000-03035, OMICS_01694, r3d100010798 | https://doi.org/10.17616/R3FS61 | SCR_006695 | InterPro: protein sequence analysis & classification, InterPro protein sequence analysis and classification | 2026-09-05 06:25:59 | 7722 | ||||
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Pseudomonas Genome Database Resource Report Resource Website 500+ mentions |
Pseudomonas Genome Database (RRID:SCR_006590) | PseudoCAP | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Database of peer-reviewed, continually updated annotation for the Pseudomonas aeruginosa PAO1 reference strain genome expanded to include all Pseudomonas species to facilitate cross-strain and cross-species genome comparisons with high quality comparative genomics. The database contains robust assessment of orthologs, a novel ortholog clustering method, and incorporates five views of the data at the sequence and annotation levels (Gbrowse, Mauve and custom views) to facilitate genome comparisons. Other features include more accurate protein subcellular localization predictions and a user-friendly, Boolean searchable log file of updates for the reference strain PAO1. The current annotation is updated using recent research literature and peer-reviewed submissions by a worldwide community of PseudoCAP (Pseudomonas aeruginosa Community Annotation Project) participating researchers. If you are interested in participating, you are invited to get involved. Many annotations, DNA sequences, Orthologs, Intergenic DNA, and Protein sequences are available for download. | gene, genome, annotation, localization, prokaryote, pseudomonas aeruginosa, sequence, subcellular, cystic fibrosis, ortholog, annotation, dna sequence, intergenic dna, protein sequence, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: Debian is listed by: bio.tools is related to: AmiGO has parent organization: Simon Fraser University; British Columbia; Canada has parent organization: University of British Columbia; British Columbia; Canada |
Cystic Fibrosis Foundation Therapeutics Inc | PMID:18978025 | nif-0000-03369, r3d100012086, biotools:pseudomonas_genome_database | https://bio.tools/pseudomonas_genome_database, https://doi.org/10.17616/R3935H | SCR_006590 | Pseudomonas Genome Database - Improving Disease Treatment Through Genome Research | 2026-09-05 06:25:57 | 543 | |||||
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MaizeGDB Resource Report Resource Website 1000+ mentions |
MaizeGDB (RRID:SCR_006600) | MaizeGDB | analysis service resource, data analysis service, data or information resource, data repository, database, organism-related portal, portal, production service resource, service resource, storage service resource, topical portal | Collection of data related to crop plant and model organism Zea mays. Used to synthesize, display, and provide access to maize genomics and genetics data, prioritizing mutant and phenotype data and tools, structural and genetic map sets, and gene models and to provide support services to the community of maize researchers. Data stored at MaizeGDB was inherited from the MaizeDB and ZmDB projects. Sequence data are from GenBank. Data are searchable by phenotype, traits, Pests, Gel Pattern, and Mutant Images. | zea mays, corn, model organism, genome, locus, metabolic pathway, genetics, genomics, sequence, gene product, function, literature reference, phenotype, trait, pest, gel pattern, mutant, blast, gene, image, corn, genotype-environment interaction, gene mapping, plant genome mapping, plant genome, gold standard, bio.tools, FASEB list |
is listed by: re3data.org is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: GenBank has parent organization: University of Maryland; Maryland; USA works with: Maize Database of Images and Genomes |
National Corn Growers Association ; NSF ; USDA/ARS ; USDA |
PMID:21624896 PMID:18769488 PMID:15888678 PMID:14681441 |
Free, Freely available, Acknowledgement requested, The community can contribute to this resource | OMICS_01655, biotools:MaizeDIG, nif-0000-03096, r3d100010795 | https://bio.tools/MaizeDIG, https://doi.org/10.17616/R3V32B | SCR_006600 | Maize Genetics and Genomics Database, MaizeGDB, MaizeGDB Locus | 2026-09-05 06:25:57 | 1047 | ||||
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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 | 2026-09-05 06:25:59 | 1 | ||||||
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GASiC Resource Report Resource Website 1+ mentions |
GASiC (RRID:SCR_006765) | GASiC | software resource | A method to correct read alignment results for the ambiguities imposed by similarities of genomes. | metagenome, genome, sequence, python |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:22941661 DOI:10.1093/nar/gks803 |
BSD License | OMICS_01437 | https://sources.debian.org/src/gasic/ | SCR_006765 | GASiC - Genome Abundance Similarity Correction, Genome Abundance Similarity Correction | 2026-09-05 06:26:00 | 3 | |||||
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Pre Ensembl Resource Report Resource Website 10+ mentions |
Pre Ensembl (RRID:SCR_006766) | Pre Ensembl, Pre-Ensembl, Pre!Ensembl, Pre! Ensembl | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Database of genomes that are in the process of being annotated are provided as an early access site for users. Genomes are here when the initial BLAST analysis on a new assembly has been done but the gene build has not been completed. Owing to the preliminary nature of the data, Pre-Ensembl provides views of the assembly, BLAST against the assembly and download of portions of the assembly - and little else. A number of ready-made tools for processing your data are also available. In general a full Ensembl release takes months depending on how complex the data are and the time constraints of people in the team. Occasionally a more complete gene build will be released on this site, but without any comparative genomics, variation or other additional data. Many other species with fully annotated genomic data, more website features and documentation are available at www.ensembl.org | genome, annotation, blast, blat, assembly | has parent organization: Ensembl | nlx_152112 | SCR_006766 | Ensemble Pre-release Genome Browser, Ensembl pre-build, PreEnsembl | 2026-09-05 06:26:00 | 22 | ||||||||
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Cscan Resource Report Resource Website 1+ mentions |
Cscan (RRID:SCR_006756) | Cscan | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Data resource that includes a large collection of genome-wide ChIP-Seq experiments performed on transcription factors (TFs), histone modifications, RNA polymerases and others. Enriched peak regions from the ChIP-Seq experiments are crossed with the genomic coordinates of a set of input genes, to identify which of the experiments present a statistically significant number of peaks within the input genes' loci. The input can be a cluster of co-expressed genes, or any other set of genes sharing a common regulatory profile. Users can thus single out which TFs are likely to be common regulators of the genes, and their respective correlations. Also, by examining results on promoter activation, transcription, histone modifications, polymerase binding and so on, users can investigate the effect of the TFs (activation or repression of transcription) as well as of the cell or tissue specificity of the genes' regulation and expression. | regulator, gene, genome-wide chip-seq, chip-seq, gene, genome | is listed by: OMICtools | PMID:22669907 | Free | OMICS_00529 | SCR_006756 | 2026-09-05 06:26:00 | 4 | |||||||
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ENCODE Resource Report Resource Website 1000+ mentions |
ENCODE (RRID:SCR_006793) | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | Encyclopedia of DNA elements consisting of list of functional elements in human genome, including elements that act at protein and RNA levels, and regulatory elements that control cells and circumstances in which gene is active. Enables scientific and medical communities to interpret role of human genome in biology and disease. Provides identification of common cell types to facilitate integrative analysis and new experimental technologies based on high-throughput sequencing. Genome Browser containing ENCODE and Epigenomics Roadmap data. Data are available for entire human genome. | Encyclopedia, DNA, element, functional, human, genome, protein, RNA, level, regulatory, gene, active, disease, analysis |
uses: Segway - a way to segment the genome is used by: BioSample Database at EBI is used by: VizHub is used by: GEMINI is used by: Deep Blue Epigenomic Data Server is recommended by: National Library of Medicine is listed by: OMICtools is affiliated with: GENCODE is related to: Factorbook is related to: UCSC Genome Browser is related to: modENCODE is related to: UCSC Genome Browser is related to: Encode is related to: Broad Institute Genomics Platform has parent organization: University of California at Santa Cruz; California; USA |
NHGRI | PMID:21526222 | Free, Freely available | nif-0000-02797, r3d100013051, SCR_017493, OMICS_00532 | http://encodeproject.org/ENCODE/, https://www.genome.gov/Funded-Programs-Projects/ENCODE-Project-ENCyclopedia-Of-DNA-Elements, https://www.encodeproject.org/, https://doi.org/10.17616/R31NJMKB | SCR_006793 | ENCODE - Encyclopedia of DNA Elements, ENCODE + Epigenomics Roadmap Combined Data Browser, Encyclopedia of DNA Elements, Encyclopedia of DNA Elements (ENCODE) | 2026-09-05 06:26:01 | 4206 | |||||
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1000 Genomes: A Deep Catalog of Human Genetic Variation Resource Report Resource Website 5000+ mentions |
1000 Genomes: A Deep Catalog of Human Genetic Variation (RRID:SCR_006828) | 1000 Genomes | consortium, data or information resource, data set, database, organization portal, portal | International collaboration producing an extensive public catalog of human genetic variation, including SNPs and structural variants, and their haplotype contexts, in an effort to provide a foundation for investigating the relationship between genotype and phenotype. The genomes of about 2500 unidentified people from about 25 populations around the world were sequenced using next-generation sequencing technologies. Redundant sequencing on various platforms and by different groups of scientists of the same samples can be compared. The results of the study are freely and publicly accessible to researchers worldwide. The consortium identified the following populations whose DNA will be sequenced: Yoruba in Ibadan, Nigeria; Japanese in Tokyo; Chinese in Beijing; Utah residents with ancestry from northern and western Europe; Luhya in Webuye, Kenya; Maasai in Kinyawa, Kenya; Toscani in Italy; Gujarati Indians in Houston; Chinese in metropolitan Denver; people of Mexican ancestry in Los Angeles; and people of African ancestry in the southwestern United States. The goal Project is to find most genetic variants that have frequencies of at least 1% in the populations studied. Sequencing is still too expensive to deeply sequence the many samples being studied for this project. However, any particular region of the genome generally contains a limited number of haplotypes. Data can be combined across many samples to allow efficient detection of most of the variants in a region. The Project currently plans to sequence each sample to about 4X coverage; at this depth sequencing cannot provide the complete genotype of each sample, but should allow the detection of most variants with frequencies as low as 1%. Combining the data from 2500 samples should allow highly accurate estimation (imputation) of the variants and genotypes for each sample that were not seen directly by the light sequencing. All samples from the 1000 genomes are available as lymphoblastoid cell lines (LCLs) and LCL derived DNA from the Coriell Cell Repository as part of the NHGRI Catalog. The sequence and alignment data generated by the 1000genomes project is made available as quickly as possible via their mirrored ftp sites. ftp://ftp.1000genomes.ebi.ac.uk ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes | genetic variation, gene, next-generation sequencing, sequence, alignment, genome, single-nucleotide polymorphism, structural variant, haplotype, genome-wide association study, pharmacology, genetics, biomarker, consortium, data sharing, genotype, phenotype, FASEB list |
uses: NHGRI Sample Repository for Human Genetic Research is used by: BioSample Database at EBI is listed by: OMICtools is listed by: re3data.org is listed by: Consortia-pedia is related to: MOSAIK is related to: ART is related to: SNAP - SNP Annotation and Proxy Search has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom has parent organization: Harvard Medical School; Massachusetts; USA has parent organization: Broad Institute has parent organization: NCBI has parent organization: European Bioinformatics Institute has parent organization: National Human Genome Research Institute |
Wellcome Trust Sanger Institute; Hinxton; United Kingdom ; Beijing Genomics Institute; Shenzhen; China ; NHGRI ; 454 Life Sciences Roche ; Life Technologies ; Illumina |
Free, Public, Restrictions apply, Http://www.1000genomes.org/data#DataAccess | r3d100010180, nlx_143819, OMICS_00261 | https://doi.org/10.17616/R3CP4M | SCR_006828 | International 1000 Genomes Project, 1000 Genomes Project | 2026-09-05 06:26:02 | 5881 | |||||
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FunNet - Transcriptional Networks Analysis Resource Report Resource Website 10+ mentions |
FunNet - Transcriptional Networks Analysis (RRID:SCR_006968) | FunNet | analysis service resource, data analysis service, data processing software, production service resource, service resource, software application, software resource | Functional Analysis of Transcriptional Networks (FunNet) is designed as an integrative tool for analyzing gene co-expression networks built from microarray expression data. The analytical model implemented in this tool involves two abstraction layers: transcriptional (i.e. gene expression profiles) and functional (i.e. biological themes indicating the roles of the analyzed transcripts). A functional analysis technique, which relies on Gene Ontology and KEGG annotations, is applied to extract a list of relevant biological themes from microarray gene expression data. Afterwards multiple-instance representations are built to relate relevant biological themes to their annotated transcripts. An original non-linear dynamical model is used to quantify the contextual proximity of relevant genomic themes based on their patterns of propagation in the gene co-expression network (i.e. capturing the similarity of the expression profiles of the transcriptional instances of annotating themes). In the end an unsupervised multiple-instance spectral clustering procedure is used to explore the modular architecture of the co-expression network by grouping together biological themes demonstrating a significant relationship in the co-expression network. Functional and transcriptional representations of the co-expression network are provided, together with detailed information on the contextual centrality of related transcripts and genomic themes. FunNet is provided both as a web-based tool and as a standalone R package. The standalone R implementation can be run on any operating system for which an R environment implementation is available (Windows, Mac OS, various flavors of Linux and Unix) and can be downloaded from the FunNet website, or from the worldwide mirrors of CRAN. Both implementations of the FunNet tool are provided freely under the GNU General Public License 2.0. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | genome, transcriptional interaction, microarray, gene expression, statistical analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: KEGG has parent organization: Cordelier Research Center |
PMID:18208606 | Free for academic use, GNU General Public License, v2 | nlx_149243 | SCR_006968 | Functional Analysis of Transcriptional Networks, Functional Analysis of Transcriptional Networks (FunNet) | 2026-09-05 06:26:04 | 17 | ||||||
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HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism Resource Report Resource Website 50+ mentions |
HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism (RRID:SCR_007050) | HumanCyc | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource, software resource | The HumanCyc database describes human metabolic pathways and the human genome. By presenting metabolic pathways as an organizing framework for the human genome, HumanCyc provides the user with an extended dimension for functional analysis of Homo sapiens at the genomic level. A computational pathway analysis of the human genome assigned human enzymes to predicted metabolic pathways. Pathway assignments place genes in their larger biological context, and are a necessary step toward quantitative modeling of metabolism. HumanCyc contains the complete genome sequence of Homo sapiens, as presented in Build 31. Data on the human genome from Ensembl, LocusLink and GenBank were carefully merged to create a minimally redundant human gene set to serve as an input to SRI''s PathoLogic software, which generated the database and predicted Homo sapiens metabolic pathways from functional information contained in the genome''s annotation. SRI did not re-annotate the genome, but worked with the gene function assignments in Ensembl, LocusLink, and GenBank. The resulting pathway/genome database (PGDB) includes information on 28,783 genes, their products and the metabolic reactions and pathways they catalyze. Also included are many links to other databases and publications. The Pathway Tools software/database bundle includes HumanCyc and the Pathway Tools software suite and is available under license. This form of HumanCyc is faster and more powerful than the Web version. | enzyme, function, functional, gene, genome, genomic, human, human genome, metabolic, metabolism, mitochondrion, nucleotide, pathway, position, reaction, sequence, metabolomics, gene expression, bioreaction, metabolic pathway, nutrition, FASEB list |
is listed by: BioCyc is related to: Pathway Commons is related to: ConsensusPathDB is related to: BioCyc is related to: Pathway Tools has parent organization: Stanford Research Institute International |
Pharmaceutical company ; NIGMS GM092729 |
PMID:15642094 | Public | r3d100011286, nif-0000-21206 | https://doi.org/10.17616/R3ZS72 | SCR_007050 | 2026-09-05 06:26:06 | 65 | |||||
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TriTrypDB Resource Report Resource Website 500+ mentions |
TriTrypDB (RRID:SCR_007043) | TriTrypDB | analysis service resource, data access protocol, data analysis service, data or information resource, database, production service resource, service resource, software resource, web service | An integrated genomic and functional genomic database providing access to genome-scale datasets for kinetoplastid parasites, and supporting a variety of complex queries driven by research and development needs. Currently, TriTrypDB integrates datasets from Leishmania braziliensis, L. infantum, L. major, L. tarentolae, Trypanosoma brucei and T. cruzi. Users may examine individual genes or chromosomal spans in their genomic context, including syntenic alignments with other kinetoplastid organisms. Data within TriTrypDB can be interrogated utilizing a sophisticated search strategy system that enables a user to construct complex queries combining multiple data types. All search strategies are stored, allowing future access and integrated searches. ''''User Comments'''' may be added to any gene page, enhancing available annotation; such comments become immediately searchable via the text search, and are forwarded to curators for incorporation into the reference annotation when appropriate. TriTrypDB provides programmatic access to its searches, via REST Web Services. The result of a web service request is a list of records (genes, ESTs, etc) in either XML or JSON format. REST services can be executed in a browser by typing a specific URL. TriTrypDB and its continued development are possible through the collaborative efforts between EuPathDB, GeneDB and colleagues at the Seattle Biomedical Research Institute (SBRI). | kinetoplastid parasite, pathogen, genome, gene chromosome, annotation, trypanosomatidae, parasite, blast, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: GeneDB is related to: GeneDB Lmajor is related to: GeneDB Tbrucei has parent organization: Eukaryotic Pathogen Database Resources |
Bill and Melinda Gates Foundation 50097; Wellcome Trust WT085822MA; Wellcome Trust WT085775/Z/08/Z |
PMID:19843604 | Public - please cite. Much of the data in TriTrypDB is provided by independent researchers. Please cite them if you use their data. | nlx_152064, biotools:tritrypdb, r3d100011479 | https://bio.tools/tritrypdb, https://doi.org/10.17616/R3J05N | SCR_007043 | 2026-09-05 06:26:06 | 712 |
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