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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
PiGx
 
Resource Report
Resource Website
1+ mentions
PiGx (RRID:SCR_016476) PiGx data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit Software application as a collection of genomic pipelines used for raw fastq read data of bisulfite experiments, RNAseq samples, single cell dropseq analysis, reads from ChIPseq experiments, analysis of sequence mutations in CRISPR-CAS9 targeted amplicon sequencing data. collection, genomic, pipeline, bisulfite, sequencing, rnaseq, chipseq, single, cell, reproducibility, sample, analysis, mutation, data European Union Horizon 2020 No 654248;
German Federal Ministry of Education and Research (BMBF) 031 A538C RBC (de.NBI)
Free, Available for download, Freely available https://github.com/BIMSBbioinfo/pigx SCR_016476 Pipelines in Genomics 2026-09-12 12:58:40 6
IndelGenotyper
 
Resource Report
Resource Website
50+ mentions
IndelGenotyper (RRID:SCR_016663) GATK data analysis software, data processing software, sequence analysis software, software application, software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18th,2023. Software package for genome analysis. Used for analysis of next generation genomic data in cancer. next, generation, analysis, genomic, data, cancer, genome is listed by: Debian
has parent organization: Broad Institute
THIS RESOURCE IS NO LONGER IN SERVICE https://github.com/broadinstitute/gatk/, https://sources.debian.org/src/gatk/ SCR_016663 GATK Indel Genotyper, Genome Analysis Toolkit (GATK) Indel Genotyper, Indel Genotyper, GATK IndelGenotyper 2026-09-12 12:58:43 88
Entrez
 
Resource Report
Resource Website
10+ mentions
Entrez (RRID:SCR_016640) data access protocol, data or information resource, portal, software resource, web service Web portal for global query cross database search and retrieval system that provides access to all databases simultaneously with a single query string and user interface. Retrieves nucleotide and protein sequence data, gene centered and genomic mapping information, 3D structures, and references. Covers databases including protein sequence data from PIR-International, PRF, Swiss-Prot, and PDB and nucleotide sequence data from GenBank that includes information from EMBL and DDBJ. global, query, cross, database, search, retrival, system, database, nucleotide, protein, sequence, data, genomic, mapping, structure, reference is affiliated with: PubChem BioAssay
is related to: National Library of Medicine
has parent organization: NCBI
works with: Batch Entrez
works with: Biotite
Free, Freely available SCR_016640 2026-09-12 12:58:42 17
GenomicFeatures
 
Resource Report
Resource Website
50+ mentions
GenomicFeatures (RRID:SCR_016960) data analysis software, data processing software, software application, software resource, software toolkit Software R package for making and manipulating transcript centric annotations. Used to download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database. making, manipulating, transcript, centric, annotation, genomic, location, exon, cds, bio.tools is used by: riboWaltz
is listed by: Bioconductor
is listed by: Debian
is listed by: bio.tools
is related to: R Project for Statistical Computing
NHGRI P41 HG004059;
NHGRI U41 HG004059;
NHLBI R01 HL086601;
NHLBI R01 HL093076;
NHLBI R01 HL094635
PMID:23950696 Free, Available for download, Freely available biotools:genomicfeatures https://bio.tools/genomicfeatures SCR_016960 2026-09-12 12:58:46 71
LDHEATMAP
 
Resource Report
Resource Website
100+ mentions
LDHEATMAP (RRID:SCR_006312) software application, software resource Software application that plots measures of pairwise linkage disequilibria for SNPs (entry from Genetic Analysis Software) gene, genetic, genomic, r is listed by: Genetic Analysis Software nlx_154424, SCR_009347, nlx_154561 http://stat-db.stat.sfu.ca:8080/statgen/research/LDheatmap SCR_006312 R/LDHEATMAP 2026-09-12 01:00:56 169
Gene Expression Profile Analysis Suite
 
Resource Report
Resource Website
10+ mentions
Gene Expression Profile Analysis Suite (RRID:SCR_008341) data processing software, software application, software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. An integrated packages of tools for microarray data analysis. GEPAS provides a web-based interface that offers diverse analysis options from the early step of preprocessing (normalization of Affymetrix and two-color microarray experiments and other preprocessing options), to the final step of the functional profiling of the experiment (using Gene Ontology, pathways, PubMed abstracts etc.), which include different possibilities for clustering, gene selection, class prediction and array-comparative genomic hybridization management. expression, gene, analysis, genomic, microarray, microarray platform, prediction, data set is listed by: 3DVC
has parent organization: Principe Felipe Research Centre; Valencia; Spain
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-25201 SCR_008341 Gepas 2026-09-12 01:00:58 20
HCLUST
 
Resource Report
Resource Website
1000+ mentions
HCLUST (RRID:SCR_009154) HCLUST software application, software resource Software application that is a simple clustering method that can be used to rapidly identify a set of tag SNP's based upon genotype data (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. gene, genetic, genomic, r, bio.tools is listed by: Genetic Analysis Software
is listed by: bio.tools
is listed by: Debian
THIS RESOURCE IS NO LONGER IN SERVICE biotools:h-clust, SCR_009102, nlx_154195, nlx_154331 https://bio.tools/h-clust SCR_009154 R/HCLUST 2026-09-12 01:00:59 1460
NCBI YouTube Channel
 
Resource Report
Resource Website
NCBI YouTube Channel (RRID:SCR_006084) NCBI YouTube Channel data or information resource, video resource Videos from the National Center for Biotechnology Information including presentations and tutorials about NCBI biomolecular and biomedical literature databases and tools. biomolecule, biomedicine, database, tool, genome, biomedical, genomic, molecular biology, genome, health, disease has parent organization: NCBI nlx_151495 SCR_006084 2026-09-12 01:01:41 0
Yeast Search for Transcriptional Regulators And Consensus Tracking
 
Resource Report
Resource Website
100+ mentions
Yeast Search for Transcriptional Regulators And Consensus Tracking (RRID:SCR_006076) YEASTRACT data or information resource, database A curated repository of more than 206000 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1300 bibliographic references. It also includes the description of 326 specific DNA binding sites shared among 113 characterized TFs. Further information about each Yeast gene has been extracted from the Saccharomyces Genome Database (SGD). For each gene the associated Gene Ontology (GO) terms and their hierarchy in GO was obtained from the GO consortium. Currently, YEASTRACT maintains a total of 7130 terms from GO. The nucleotide sequences of the promoter and coding regions for Yeast genes were obtained from Regulatory Sequence Analysis Tools (RSAT). All the information in YEASTRACT is updated regularly to match the latest data from SGD, GO consortium, RSA Tools and recent literature on yeast regulatory networks. YEASTRACT includes DISCOVERER, a set of tools that can be used to identify complex motifs found to be over-represented in the promoter regions of co-regulated genes. DISCOVERER is based on the MUSA algorithm. These algorithms take as input a list of genes and identify over-represented motifs, which can then be compared with transcription factor binding sites described in the YEASTRACT database. yeast, gene, regulatory association, transcription factor, target gene, genomic, transcription regulation, transcription, web service, bio.tools, FASEB list is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: SGD
is related to: Gene Ontology
is related to: Regulatory Sequence Analysis Tools
Fundacao para a Ciencia e a Tecnologia contract Pest-OE/EQB/LA0023/2011_research line: Systems and Synthetic Biology;
Fundacao para a Ciencia e a Tecnologia ERA-IB/0002/2010;
Fundacao para a Ciencia e a Tecnologia PTDC/EIA-EIA/111239/2009;
Fundacao para a Ciencia e a Tecnologia PTDC/EIA-CCO/118522/2010
PMID:24170807
PMID:20972212
PMID:18032429
PMID:16381908
Free nif-0000-03652, OMICS_00547, biotools:yeastract https://bio.tools/yeastract SCR_006076 2026-09-12 01:01:40 130
Tuberculosis Database
 
Resource Report
Resource Website
50+ mentions
Tuberculosis Database (RRID:SCR_006619) TBDB data or information resource, database Database providing integrated access to genome sequence, expression data and literature curation for Tuberculosis (TB) that houses genome assemblies for numerous strains of Mycobacterium tuberculosis (MTB) as well assemblies for over 20 strains related to MTB and useful for comparative analysis. TBDB stores pre- and post-publication gene-expression data from M. tuberculosis and its close relatives, including over 3000 MTB microarrays, 95 RT-PCR datasets, 2700 microarrays for human and mouse TB related experiments, and 260 arrays for Streptomyces coelicolor. (July 2010) To enable wide use of these data, TBDB provides a suite of tools for searching, browsing, analyzing, and downloading the data. genomic, protein, blast, genome, gene, systems biology, gene expression, microarray, comparative analysis, regulatory network, metabolic network, epitope, expression profile, rt-pcr, gene regulation, genome browser, FASEB list is listed by: re3data.org
is related to: SMD
is related to: BioCyc
has parent organization: Broad Institute
has parent organization: Stanford University School of Medicine; California; USA
Tuberculosis Bill and Melinda Gates Foundation PMID:20488753
PMID:18835847
Acknowledgement requested, Public, (Published data) nif-0000-03537, r3d100010930 https://doi.org/10.17616/R39G8F SCR_006619 TB Database, TBDatabase 2026-09-12 01:01:43 64
ViralZone
 
Resource Report
Resource Website
100+ mentions
ViralZone (RRID:SCR_006563) ViralZone data or information resource, database ViralZone is a SIB Swiss Institute of Bioinformatics web-resource for all viral genus and families, providing general molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives an easy access to UniProtKB/Swiss-Prot viral protein entries. ViralZone project is handled by the virus program of SwissProt group. Proteins popups were developed in collaboration with Prof. Christian von Mering and Andrea Franceschini, Bioinformatics Group , Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland, funded in part by the SIB Swiss Institute of bioinformatics. All pictures in ViralZone are copyright of the SIB Swiss Institute of Bioinformatics. dna virus, rna virus, virus, dna, rna, genomic, proteomic, sequence, reference strain, image, virion, retro-transcribing virus, genome, bibliographic, bio.tools is listed by: Debian
is listed by: bio.tools
has parent organization: SIB Swiss Institute of Bioinformatics
Swiss Institute of Bioinformatics PMID:20947564 biotools:viralzone, r3d100013314, nlx_144372 https://bio.tools/viralzone, https://doi.org/10.17616/R31NJMRM http://www.expasy.org/viralzone/ SCR_006563 Viral Zone 2026-09-12 01:01:43 148
waviCGH
 
Resource Report
Resource Website
1+ mentions
waviCGH (RRID:SCR_006662) waviCGH analysis service resource, data analysis service, production service resource, service resource A versatile web-server application for the analysis and visualization of array-CGH data. genomic, copy number alteration, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
PMID:20507915 Acknowledgement requested OMICS_00739, biotools:wavicgh https://bio.tools/wavicgh SCR_006662 2026-09-12 01:01:43 4
ProbeExplorer
 
Resource Report
Resource Website
ProbeExplorer (RRID:SCR_007116) ProbeExplorer analysis service resource, data analysis service, production service resource, service resource Probe Explorer is an open access web-based bioinformatics application designed to show the association between microarray oligonucleotide probes and transcripts in the genomic context, but flexible enough to serve as a simplified genome and transcriptome browser. Coordinates and sequences of the genomic entities (loci, exons, transcripts), including vector graphics outputs, are provided for fifteen metazoa organisms and two yeasts. Alignment tools are used to built the associations between Affymetrix microarrays probe sequences and the transcriptomes (for human, mouse, rat and yeasts). Search by keywords is available and user searches and alignments on the genomes can also be done using any DNA or protein sequence query. Platform: Online tool bioinformatics, microarray, oligonucleotide probe, transcript, genomic, genome, transcriptome, alignment, affymetrix, probe sequence, dna, protein, sequence, statistical analysis is listed by: Gene Ontology Tools
is related to: Gene Ontology
has parent organization: University of Salamanca; Salamanca; Spain
Open unspecified license - Free for academic use nlx_149275 SCR_007116 Probe Explorer 2026-09-12 01:01:45 0
Tetraodon nigroviridis Database
 
Resource Report
Resource Website
Tetraodon nigroviridis Database (RRID:SCR_007123) data or information resource, database This database have been funded by the National Human Genome Research Institute (NHGRI) to produce shotgun sequence of the Tetraodon nigriviridis genome. The strategy involves Whole Genome Shotgun (WGS) sequencing, in which sequence from the entire genome is generated. Whole genome shotgun libraries were prepared from Tetraodon genomic DNA obtained from the laboratory of Jean Weissenbach at Genoscope. Additional sequence data of approximately 2.5X coverage of Tetraodon has also been generated by Genoscope in plasmid and BAC end reads. Broad and Genoscope intend to pool their data and generate whole genome assemblies. Tetraodon nigroviridis is a freshwater pufferfish of the order Tetraodontiformes and lives in the rivers and estuaries of Indonesia, Malaysia and India. This species is 20-30 million years distant from Fugu rubripes, a marine pufferfish from the same family. The gene repertoire of T. nigroviridis is very similar to that of other vertebrates. However, its relatively small genome of 385 Mb is eight times more compact than that of human, mostly because intergenic and intronic sequences are reduced in size compared to other vertebrate genomes. These genome characteristics along with the large evolutionary distance between bony fish and mammals make Tetraodon a compact vertebrate reference genome - a powerful tool for comparative genetics and for quick and reliable identification of human genes. estruary, evolutionary, fish, freshwater, fugu rubripes, gene, genetic, bac, bony, distance, dna, genome, genomic, human, intergenic, intronic, nigriviridis, plasmid, pufferfish, river, sequence, sequencing, shotgun, specie, tetraodon, tetraodontiformes, vertebrate nif-0000-20998 SCR_007123 TND 2026-09-12 01:01:45 0
SpBase - Strongylocentrotus purpuratus: the Sea Urchin Genome Database
 
Resource Report
Resource Website
1+ mentions
SpBase - Strongylocentrotus purpuratus: the Sea Urchin Genome Database (RRID:SCR_007441) SpBase data or information resource, database, image SpBase is designed to present the results of the genome sequencing project for the purple sea urchin. The sequences and annotations emerging from this effort are organized in a database that provides the research community access to those data not normally presented through National Center for Biotechnology Information and other large databases. Additionally, the unique information on that links gene identities and sequences to the plate and well location to the library filters from the Sea Urchin genome Resource will also be presented. The software used to organize and present the sea urchin genome comes from GMOD, a collection of open source software tools for creating and managing genome-scale biological databases. That sea urchins eggs and embryos have long remained a popular research subject for cell and developmental biologists is one rationale for sequencing the genome. In addition, studies of embryonic development in the California Purple Sea Urchin, Strongylocentrotus purpuratus , have paralleled the emergence of molecular techniques ranging from the characterization of genomic repeat sequences in the 1970''s to the elucidation of gene regulatory networks in recent times. The parent of this site, SUGP, was meant to provide a focal point for the exchange of genomic information as the genome of the Purple sea urchin was being sequenced. Over these past years it has served as a repository for small sequencing projects and a source of sequence information useful for gene discovery projects. Here one could find information on macro-array libraries of cDNAs from the purple sea urchin and genomic DNA from several species. In addition, a Sequence Tag Connector (STC) collection has been assembled from 5% of the genome sequence and a very extensive repeat sequence catalog prepared. All of the sequence data that we maintained at SUGP was incorporated into the new SPBase. Of course, it is all in public sequence databases such as the National Center for Biological Information as well. Some additional sequence information is available at the Resource Center of the German Human Genome Project. With the publication of The Genome of the Sea Urchin Strongylocentrotus purpuratus by The Sea Urchin Genome Sequencing Consortium a link to the first 9941 gene annotations are now publicly available. The effort to sequence the whole purple sea urchin genome was a cooperative one that included contributions from the Sea Urchin Genome Facility here at the Center for Computational Regulatory Genomics, Beckman Institute, Caltech, and support from the Human Genome Research Institute of the National Institutes of Health. The sequencing was done at the Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas. Funding was approved based on an initiative submitted by the Sea Urchin Genome Advisory Committee. embryonic, genome, annotation, bac, cdna, clones, development, dna, genomic, genomic library, images, macro-array libraries, sequence tag connector, sequencing, stc, strongylocentrotus purpuratus nif-0000-01282 http://sugp.caltech.edu SCR_007441 SpBase - Strongylocentrotus purpuratus, Sea Urchin Genome Database 2026-09-12 01:01:47 4
Mammalian Degradome Database
 
Resource Report
Resource Website
10+ mentions
Mammalian Degradome Database (RRID:SCR_007624) Degradome Database data or information resource, database A database of human, chimpanzee, mouse, and rat proteases and protease inhibitors, as well as as the growing number of hereditary diseases caused by mutations in protease genes. Analysis of the human and mouse genomes has allowed us to annotate 581 human, 580 chimpanzee, 667 mouse, and 655 rat protease genes. Proteases are classified in five different classes according to their mechanism of catalysis. Proteases are a diverse and important group of enzymes representing >2% of the human, chimpanzee, mouse and rat genomes. This group of enzymes is implicated in numerous physiological processes. The importance of proteases is illustrated by the existence of 99 different hereditary diseases due to mutations in protease genes. Furthermore, proteases have been implicated in multiple human pathologies, including vascular diseases, rheumatoid arthritis, neurodegenerative processes, and cancer. During the last ten years, our laboratory has identified and characterized more than 60 human protease genes. Due to the importance of proteolytic enzymes in human physiology and pathology, we have recently introduced the concept of Degradome, as the complete repertoire of proteases expressed by a tissue or organism. Thanks to the recent completion of the human, chimpanzee, mouse, and rat genome sequencing projects, we were able to analyze and compare for the first time the complete protease repertoire in those mammalian organisms, as well as the complement of protease inhibitor genes. This webpage also contains the Supplementary Material of Human and mouse proteases: a comparative genomic approach Nat Rev Genet (2003) 4: 544-558, Genome sequence of the brown Norway rat yields insights into mammalian evolution Nature (2004) 428: 493-521, A genomic analysis of rat proteases and protease inhibitors Genome Res. (2004) 14: 609-622, and Comparative genomic analysis of human and chimpanzee proteases Genomics (2005) 86: 638-647. degradome, mammalian, protease inhibitor, protease, gene, protease gene, genetic disease, proteolysis, protease structure, ancillary domain, genomic, genome is related to: Ancillary Domains Associated With Human and Mouse Proteases
has parent organization: University of Oviedo; Oviedo; Spain
Disease of proteolysis European Union ;
CancerDegradome-FP6 and FP7 ;
Spanish Ministry of Science and Innovation ;
Fundacion M Botin ;
Fundacion Lilly ;
Obra Social Cajastur
PMID:18776217 nif-0000-02746 SCR_007624 Mammalian Degradome Database 2026-09-12 01:01:49 10
Organelle Genome Resources
 
Resource Report
Resource Website
1+ mentions
Organelle Genome Resources (RRID:SCR_007838) data or information resource, database Curated sequence data and related information on organelles from NCBI Refseq for the community to use as a standard. The animal mitochondrial records are considered reviewed; that is, they have been manually curated by the NCBI staff. Other mitochondrial and chloroplast genome records are provisional and are presented with varying levels of review compared to the primary record used to build the RefSeq. Additionally, protein clusters for the metazoan and plastid genomes proteins can be reviewed with Entrez Protein Clusters. mitochondrion, chloroplast, refseq, genomic, gene sequence, gene has parent organization: NCBI nif-0000-03227 http://www.ncbi.nlm.nih.gov/genomes/ORGANELLES/organelles.html SCR_007838 Organelle Genome Resources 2026-09-12 01:01:53 4
University of California Los Angeles Technology Center for Genomics and Bioinformatics Core Facility
 
Resource Report
Resource Website
1+ mentions
University of California Los Angeles Technology Center for Genomics and Bioinformatics Core Facility (RRID:SCR_012204) TCGB, UCLA TCGB, access service resource, core facility, service resource Core is a fully automated, high-throughput genomic Center equipped with next generation sequencing and microarray platforms. TCGB provides genomics technologies, comprehensive services, specialized expertise and a wide range of trainings, enabling these services to serve basic science and translational/clinical research. In addition, TCGB provides pre-experiment consultation and post-experiment support, including preparation of grant applications, publications, and strategic planning for additional research steps. TCGB also provides educational training to faculty, staff, and students to raise awareness of new directions and major discoveries in the areas of genomics and bioinformatics. training, genomic, next generation sequencing, microarray platforms, is listed by: ScienceExchange
is related to: University of California Los Angeles Labs and Facilities
has parent organization: University of California at Los Angeles; California; USA
Open SciEx_10586 http://www.scienceexchange.com/facilities/clinical-microarray-core-ucla http://pathology.ucla.edu/tcgb SCR_012204 University of California Los Angeles, University of California Los Angeles Technology Center for Genomics & Bioinformatics 2026-09-12 01:03:38 5
DFCI Center for Cancer Computational Biology
 
Resource Report
Resource Website
DFCI Center for Cancer Computational Biology (RRID:SCR_012688) DFCI CCCB access service resource, core facility, service resource Core facility that provides the following services: Microarray and other genomic data analysis, MiSeq. The Center provides broad-based support for the generation, analysis, and interpretation of genomic and other large-scale data in the context of basic, clinical and translational research. The CCCB has three primary elements. * The CCCB sequencing facility offers a wide range of services to assist in the design and execution of next-generation sequencing projects. Utilizing the Illumina (Solexa) sequencing technology, they currently support a number of applications inlcuding ChIP-Seq, RNA-Seq, whole genome, whole exome, and targeted re-sequencing. * The analytical services and support platform aims to provide state-of-the-art assistance in the collection, management, analysis, and interpretation of large-scale data with a focus on data generated using ''''omic technologies. In addition, they offer software, services, and training designed to assist investigators in advancing their research. * The CCCB research program is focused on development of new methods for improving analysis and interpretation of genomic data through integration of diverse data types with the goal of creating open-source software tools to be made freely-available to the research community. nucleic acid microarray assay, next generation sequencing, genome, genomic, microarray is listed by: ScienceExchange
is listed by: Eagle I
is related to: Dana-Farber Cancer Institute Labs and Facilities
has parent organization: Dana-Farber Cancer Institute
Cancer SciEx_8878 http://harvard.eagle-i.net/i/0000012e-59a5-5f86-55da-381e80000000, http://www.scienceexchange.com/facilities/center-for-cancer-computational-biology-cccb-harvard SCR_012688 Dana-Farber Cancer Institute Center for Cancer Computational Biology, DFCI Center for Cancer Computational Biology (CCCB) 2026-09-12 01:03:45 0
Nutrition and Obesity Research Centers at Harvard Genomics and Cell Biology Core
 
Resource Report
Resource Website
Nutrition and Obesity Research Centers at Harvard Genomics and Cell Biology Core (RRID:SCR_015427) NORCH, NORCH at Harvard, access service resource, core facility, resource, service resource Core that facilitates the application of genomics, bioinformatics, cell biology, and immunology techniques to nutrition and metabolic research. genomic, cell biology, bioinformatic, immunology, nutrition, metabolic is listed by: NIDDK Information Network (dkNET)
has parent organization: Harvard Medical School; Massachusetts; USA
has parent organization: Nutrition and Obesity Research Centers at Harvard
is organization facet of: Nutrition and Obesity Research Centers at Harvard
Obesity NIDDK P30 DK046200 Available to external user SCR_015427 NORCH, Genomics and Cell Biology Core, Harvard, Nutrition and Obesity Research Center 2026-09-12 01:03:56 0

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