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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MiTCR Resource Report Resource Website 10+ mentions |
MiTCR (RRID:SCR_004989) | MiTCR | software resource | An open source software package aimed at extraction of information on repertoire of T-cell clones from Next Generation Sequencing (NGS) data. It is designed with the knowledge of the critical challenges arising in everyday processing of immunological data. | next generation sequencing | is listed by: OMICtools | PMID:23892897 | Apache License | OMICS_00003 | SCR_004989 | MiTCR - T-cell receptor repertoire analysis software | 2026-08-15 11:23:04 | 37 | ||||||
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MIP Scaffolder Resource Report Resource Website 1+ mentions |
MIP Scaffolder (RRID:SCR_005072) | MIP Scaffolder | software resource | A software program for scaffolding contigs produced by fragment assemblers using mate pair data such as those generated by ABI SOLiD or Illumina Genome Analyzer. | scaffolding, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Helsinki; Helsinki; Finland |
OMICS_00044, biotools:mip_scaffolder | https://bio.tools/mip_scaffolder | SCR_005072 | 2026-08-15 11:22:58 | 1 | ||||||||
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Scarpa Resource Report Resource Website 10+ mentions |
Scarpa (RRID:SCR_005073) | Scarpa | software resource | A stand-alone scaffolding tool for NGS data. It can be used together with virtually any genome assembler and any NGS read mapper that supports SAM format. Other features include support for multiple libraries and an option to estimate insert size distributions from data. | scaffolding |
is listed by: OMICtools has parent organization: University of Toronto; Ontario; Canada |
PMID:23274213 | GNU General Public License | OMICS_00047 | SCR_005073 | SCARPA: scaffolding reads with practical algorithms, Scaffolding Reads with Practical Algorithms | 2026-08-15 11:23:06 | 13 | ||||||
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NIH Neuroscience Microarray Consortium Resource Report Resource Website 1+ mentions |
NIH Neuroscience Microarray Consortium (RRID:SCR_004930) | database, production service resource, data repository, storage service resource, data analysis service, data or information resource, service resource, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 24, 2012. (no longer being funded) The NIH Microarray Consortium provides for-fee services to a community of NIH grantees, together with a more limited set of services to the public. The primary goal of this consortium is to move basic and translational research forward through acquisition and dissemination of high quality genomic data. This site includes a repository of microarray data sets and offers one-click links to public projects. These datasets were generated by various researchers on these platforms: Affymetrix, Agilent, Ambion, cDNA, Illumina, and Operon. The species currently covered are: Arabidopsis, Bovine, chicken, C. Elegans, Drosophila, Human, Macaca mulatta (Rhesus macaque), Mouse, Rat, Songbird, Xenopus, Yeast, and zebra finch. Basic search functions allows users to choose multiple options for finding the projects that interest them, and raw data files can also be downloaded after user registration. Web-based data analysis tools are also available. Scientists can analyze microarray data from the consortium repository or investigators can upload outside data for analysis. | arabidopsis, bos taurus, chicken, caenorhabditis elegans, drosophila, human, rhesus monkey, mouse, rat, songbird, xenopus, yeast, zebra finch |
is used by: NIF Data Federation is related to: Songbird Brain Transcriptome Database has parent organization: National Institutes of Health |
NIH Blueprint for Neuroscience Research | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00074 | http://arrayconsortium.tgen.org, http://np2.ctrl.ucla.edu/np2/home.do | SCR_004930 | NIH Neuroscience Microarray Consortium | 2026-08-15 11:22:55 | 4 | ||||||
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German Federal Ministry of Education and Research Resource Report Resource Website 100+ mentions |
German Federal Ministry of Education and Research (RRID:SCR_005066) | BMBF | government granting agency | SCR_005066 | Bundesministerium für Bildung und Forschung, Federal Ministry of Education and Research, Federal Ministry of Education and Research (Germany) | 2026-08-15 11:23:06 | 137 | ||||||||||||
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Alzheimer's and Dementia Resource Center Resource Report Resource Website 100+ mentions |
Alzheimer's and Dementia Resource Center (RRID:SCR_004924) | ADRC | biomaterial supply resource, tissue bank, material resource, brain bank | The Alzheimer's and Dementia Resource Center (ADRC) facilitates tissue donations for the Brain Bank Research Program in order to help find better treatments, more diagnostic tools and a cure for Alzheimer's disease and dementia. The Brain Bank Program is administered by Mount Sinai Medical Center in Miami Beach and under contract with the Florida Department of Elder Affairs. ADRC also provides caregivers with the educational resources, spiritual comfort and emotional support. The ADRC facilitates training for professional caregivers that meets requirements for the Florida Department of Elder Affairs. | alzheimer's disease, dementia, brain, tissue, brain bank, caregiver, educational resource, patient support | is listed by: One Mind Biospecimen Bank Listing | Alzheimer's disease, Dementia | Public, Registration and pre-registration required to access the brain bank | nlx_143948 | SCR_004924 | alzheimer's disease, tissue, brain, patient support, educational resource, caregiver, dementia, brain bank | 2026-08-15 11:23:07 | 421 | ||||||
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PhenomeBLAST Ontology Resource Report Resource Website 1+ mentions |
PhenomeBLAST Ontology (RRID:SCR_005139) | PHENOMEBLAST | ontology, data or information resource, controlled vocabulary | A cross-species phenotype and anatomy ontology resulting from combining available anatomy and phenotype ontologies and their definitions. The ontology includes phenotype definitions for yeast, mouse, fish, worm, fly and human phenotypes and diseases. | owl | is listed by: BioPortal | nlx_157549 | SCR_005139 | 2026-08-15 11:23:08 | 1 | |||||||||
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T-lex Resource Report Resource Website 1+ mentions |
T-lex (RRID:SCR_005134) | T-lex | software resource | Software package for fast and accurate discovery, annotation, re-annotation and population analysis of Transposable Elements using Next-Generation Sequencing data. | transposable element, next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Stanford University; Stanford; California has parent organization: SourceForge |
GNU General Public License | biotools:t-lex2, OMICS_00121 | https://bio.tools/t-lex2 | SCR_005134 | T-lex package | 2026-08-15 11:23:08 | 4 | ||||||
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PoPoolation TE Resource Report Resource Website 1+ mentions |
PoPoolation TE (RRID:SCR_005131) | PoPoolation TE | software resource | A quick and simple pipeline for the analysis of transposable element (TE) insertions in (natural) populations using next generation sequencing. It calculates TE insertion frequencies for TEs that are present in the reference genome as well as for novel TE insertions. PoPoolation TE requires paired-end reads from a pooled population, a reference sequence and transposable element sequences (fasta-file). | next generation sequencing, transposable element, insertion frequency, genomics, population genetics, illumina |
is listed by: OMICtools has parent organization: Google Code |
PMID:22291611 | Acknowledgement requested, New BSD License | OMICS_00119 | SCR_005131 | 2026-08-15 11:23:08 | 1 | |||||||
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Alfred P. Sloan Foundation Resource Report Resource Website 50+ mentions |
Alfred P. Sloan Foundation (RRID:SCR_005099) | Sloan Foundation | institution | The Alfred P. Sloan Foundation is a philanthropic, not-for-profit grantmaking institution based in New York City. Established in 1934 by Alfred Pritchard Sloan Jr., then-President and Chief Executive Officer of the General Motors Corporation, the Foundation makes grants in support of original research and education in science, technology, engineering, mathematics and economic performance. * Promotes research in science, technology, engineering, mathematics, and economic performance * Offers two-year long research fellowships for early career researchers | grant, fellowship |
is related to: MIT Center for Biomedical Innovation is parent organization of: Datahub |
grid.453006.4, Crossref funder ID: 100000879, ISNI: 0000 0004 0508 3060, nlx_144112 | https://ror.org/052csg198 | SCR_005099 | 2026-08-15 11:22:59 | 56 | ||||||||
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Eurexpress Resource Report Resource Website 1+ mentions |
Eurexpress (RRID:SCR_005093) | Eurexpress | database, expression atlas, data or information resource, image collection, atlas | Genome transcriptome atlas by RNA in situ hybridization on sagittal sections of developing mouse at embryonic day 14.5. Consists of searchable database of annotated images that can be interactively viewed. Anatomy based expression profiles for coding genes and microRNAs, tissue specific genes. Expression data generated by using human and murine tissue arrays. | Genome, transcriptome, atlas, RNA, in situ, hybrydization, sagittal, section, developing, mouse, embryo, expression, gene |
is listed by: GUDMAP Ontology is listed by: NIDDK Information Network (dkNET) is related to: EMAGE Gene Expression Database is related to: aGEM has parent organization: Telethon Institute of Genetics and Medicine; Naples; Italy |
European Union ; VI Framework ; Telethon Foundation ; Swiss National Science Foundation ; Max Planck Society ; MRC ; Association pour la Recherche sur le Cancer ; Ingenio 2010 MEuropean Union |
PMID:21267068 | nif-0000-00243 | http://www.eurexpress.org/ee/databases/anatomy/treeFrames.jsp, http://www.eurexpress.org/ee/ | SCR_005093 | Eurexpress atlas, Transcriptome Atlas Database for Mouse Embryo | 2026-08-15 11:23:12 | 3 | |||||
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BEERS Resource Report Resource Website 10+ mentions |
BEERS (RRID:SCR_005090) | BEERS | software resource | A simulation engine for generating RNA-Seq data that was designed to benchmark RNA-Seq alignment algorithms and also algorithms that aim to reconstruct different isoforms and alternate splicing from RNA-Seq data. By default BEERS simulates either mouse or human paired-end RNA-Seq data modeled on the illumina platform. It starts with a large number of gene models (approx 500K) taken from about ten different published annotation efforts, and then chooses a fixed number of these genes at random (30,000 by default). This avoids biasing for or against any particular set of annotations. BEERS then introduces substitutions, indels, alternate spice forms, sequencing errors, and intron signal. BEERS can also simulate strand specific reads. BEERS does not simulate quality scores. There are four configuration files required, these are available for human and mouse. BEERS can also be configured to use any set of gene models. Pre-built indexes for human refseq are given. Using these indexes will generate a much tamer set of transcripts. BEERS is written in perl. | perl, rna-seq |
is listed by: OMICtools has parent organization: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA |
PMID:21775302 | OMICS_01364 | SCR_005090 | Benchmarker for Evaluating the Effectiveness of RNA-Seq Software (BEERS), Benchmarker for Evaluating the Effectiveness of RNA-Seq Software | 2026-08-15 11:22:58 | 22 | |||||||
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University of Kiel; Schleswig-Holstein; Germany Resource Report Resource Website 1+ mentions |
University of Kiel; Schleswig-Holstein; Germany (RRID:SCR_005127) | CAU | university | A university in Germany. |
is related to: READNA is parent organization of: Transgenic Hydra Facility |
nlx_59306, Crossref funder ID:501100002869, ISNI:0000 0001 2153 9986, Wikidata:Q156737, grid.9764.c | https://ror.org/04v76ef78 | SCR_005127 | Christian-Albrechts-Universitat zu Kiel, Christian Albrechts University, University of Kiel, Christian-Albrechts-Universit�t zu Kiel, Kiel University | 2026-08-15 11:23:12 | 1 | ||||||||
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Scientific American Resource Report Resource Website 1+ mentions |
Scientific American (RRID:SCR_005243) | SA | organization portal, data or information resource, portal, narrative resource | Scientific American, the oldest continuously published magazine in the U.S., has been bringing its readers unique insights about developments in science and technology for more than 160 years. It is the leading source and authority for science, technology information and policy for a general audience. In an era of rapid innovation, Scientific American founded the first branch of the U.S. Patent Agency, in 1850, to provide technical help and legal advice to inventors. A Washington, D.C., branch was added in 1859. By 1900 more than 100,000 inventions had been patented thanks to Scientific American. * Read in print by 3.5 million worldwide consumers * On average, 2.7 million unique users visit ScientificAmerican.com every month * 14 local language editions worldwide, including the U.S. edition of Scientific American, read in more than 30 countries, with a worldwide audience of more than 5 million people * A third of Scientific American readers hold postgraduate degrees * 144 Nobel Prize Scientists have contributed 234 articles to Scientific American * Part of Macmillan Publishers, owned by Holtzbrinck Group of companies; acquired by Holtzbrinck in 1986 * Three Scientific American features in the Federal Record * Scientific American won the 2011 National Magazine Award for General Excellence. | science, technology, information, policy, magazine |
uses: InnoCentive is parent organization of: Scientific American Cross-Check is parent organization of: Scientific American Guest Blog is parent organization of: Scientific American Observations is parent organization of: Scientific American Bering in Mind |
nlx_144246 | SCR_005243 | 2026-08-15 11:23:01 | 7 | |||||||||
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ERANGE Resource Report Resource Website 10+ mentions |
ERANGE (RRID:SCR_005240) | ERANGE | software resource | Software for Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq. Its functions are to (i) assign reads that map uniquely in the genome to their site of origin and, for reads that match equally well to several sites (''multireads''), assign them to their most likely site(s) of origin; (ii) detect splice-crossing reads and assign them to their gene of origin; (iii) organize reads that cluster together, but do not map to an already known exon, into candidate exons or parts of exons; and (iv) calculate the prevalence of transcripts from each known or newly proposed RNA, based on normalized counts of unique reads, spliced reads and multireads. The new candidate RNA regions produced can be thought of as ESTs, and, like ESTs, some are provisionally appended to existing gene models if they meet several additional criteria. Remaining unassigned candidate transcribed regions (labeled RNAFAR features) can then be used in conjunction with other confirming data to develop new or revised gene models. | transcriptome, rna-seq, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:18516045 | OMICS_01274, biotools:erange | https://bio.tools/erange | SCR_005240 | Enhanced Read Analysis of Gene Expression | 2026-08-15 11:23:01 | 30 | ||||||
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RNA-SeQC Resource Report Resource Website 100+ mentions |
RNA-SeQC (RRID:SCR_005120) | RNA-SeQC | software resource | Java software which computes a series of quality control metrics for RNA-seq data and can compare sequencing quality across different samples or experiments to evaluate different experimental parameters. The input can be one or more BAM files, and the output consists of HTML reports and tab delimited files of metrics data. | java, bam file, html, sequence comparison, rnaseq, rna sequence, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Broad Institute |
PMID:22539670 | Acknowledgement requested, Public | biotools:rna-seqc, OMICS_01234 | https://bio.tools/rna-seqc | SCR_005120 | 2026-08-15 11:23:12 | 214 | ||||||
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Flux Simulator Resource Report Resource Website 1+ mentions |
Flux Simulator (RRID:SCR_005088) | Flux Simulator | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023. Software that aims at modeling RNA-Seq experiments in silico: sequencing reads are produced from a reference genome according annotated transcripts. The simulation pipeline models different steps as modules, each with a minimal set of parameters that can be estimated by experimental parameters. The first step is-in fact-a transcriptome simulator. Subsequently, common sources of systematic bias in the abundance and distribution of produced reads are simulated by in silico library preparation and sequencing. | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01365 | SCR_005088 | 2026-08-15 11:23:07 | 2 | |||||||||
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jobs.ac.uk Resource Report Resource Website 1+ mentions |
jobs.ac.uk (RRID:SCR_005154) | jobs.ac.uk | job resource | International job board for careers in academic, research, science and related professions in the UK, Europe, Australasia, Africa, America and Asia & Middle East. Launched by the University of Warwick, they have grown to become the top recruitment site in their sector, attracting the most qualified and talented people from the UK, Europe and across the world. Users may subscribe to Jobs by Email for vacancies in universities, colleges, research institutions, commercial and public sector, schools and charities. You may upload your CV to give yourself an advantage by making your CV visible to top employers now! | job seeker, employer, career, curriculum vitae, recruit, employment, database, data storage repository |
is used by: NIF Data Federation is listed by: OMICtools is related to: Integrated Jobs has parent organization: University of Warwick; Coventry; United Kingdom |
The community can contribute to this resource | OMICS_01829, nlx_144167 | SCR_005154 | 2026-08-15 11:23:09 | 3 | ||||||||
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PANTHER Evolutionary analysis of coding SNPs Resource Report Resource Website 100+ mentions |
PANTHER Evolutionary analysis of coding SNPs (RRID:SCR_005145) | cSNP Scoring | production service resource, data processing software, data analysis service, software application, data analysis software, software resource, service resource, analysis service resource | Data analysis service that estimates the likelihood of a particular nonsynonymous (amino-acid changing) coding SNP to cause a functional impact on the protein. To analyze many SNPs, download the PANTHER Coding Snp Analysis tool from the downloads page. |
is listed by: OMICtools has parent organization: PANTHER |
PMID:23193289 | OMICS_00135 | SCR_005145 | Evolutionary analysis of coding SNPs, PANTHER Coding SNP Analysis Tool | 2026-08-15 11:23:12 | 104 | ||||||||
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Project HOPE Resource Report Resource Website 10+ mentions |
Project HOPE (RRID:SCR_005141) | HOPE | production service resource, data analysis service, software resource, source code, service resource, analysis service resource | An easy-to-use webserver that analyses the structural effects of your mutation of interest. The server allows you to submit a protein sequence and the mutation. Project HOPE will then collect and combine available information from a series of webservers and databases and will produce a mutation report complete with results, figures and animations. Where available Project HOPE will use the 3D structure of the protein but the server can also build a homology model if necessary. Other information sources include the Uniprot database and a series of DAS prediction servers., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | protein structure, mutation |
is listed by: OMICtools has parent organization: Radboud University; Nijmegen; The Netherlands |
Inheritable disease | PMID:21059217 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00130 | SCR_005141 | Have yOur Protein Explained, GSITIC | 2026-08-15 11:23:12 | 29 |
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