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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Cancer Genome Anatomy Project Resource Report Resource Website 100+ mentions |
Cancer Genome Anatomy Project (RRID:SCR_003072) | CGAP | data or information resource, portal, topical portal | Project to determine the gene expression profiles of normal, precancer, and cancer cells, whose generated resources are available to the cancer community. Interconnected modules provide access to all CGAP data, bioinformatic analysis tools, and biological resources allowing the user to find in silico answers to biological questions in a fraction of the time it once took in the laboratory. * Genes * Tissues * Pathways * RNAi * Chromosomes * SAGE Genie * Tools | gene, gene expression, normal cell, precancer cell, cancer cell, cell, genome, anatomy, gene expression profile, tissue, pathway, rnai, chromosome, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: National Cancer Institute is parent organization of: CGAP GO Browser |
Cancer, Normal, Precancer | NCI | Free, download Freely available | biotools:cgap, nif-0000-30468 | https://mitelmandatabase.isb-cgc.org/mb_search | SCR_003072 | Cancer Genome Anatomy Project (CGAP) | 2026-09-12 12:55:51 | 108 | ||||
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MethDB Resource Report Resource Website 10+ mentions |
MethDB (RRID:SCR_003108) | MethDB | data or information resource, data repository, database, service resource, storage service resource | Database that provides a resource to store DNA methylation data and to make these data readily available to the public. Future development of the database will focus on environmental effects on DNA methylation. No restriction applies on the type of data, i.e. as well as global estimations (e.g. HPLC) as data from high resolution analysis (i.e. sequencing) can be stored. As much background information as possible should be provided by the users. This includes the origin of the sample, phenotype, expression of the related gene, etc.. | methylation |
is listed by: OMICtools has parent organization: University of Perpignan Via Domitia; Perpignan; France has parent organization: French National Center for Scientific Research |
PMID:11125109 PMID:17965614 PMID:12163707 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03119, OMICS_01840 | http://www.methdb.net/ | SCR_003108 | DNA Methylation Database, MethDB - the database for DNA methylation and environmental epigenetic effects | 2026-09-12 12:55:52 | 15 | |||||
|
FAS-DPD Resource Report Resource Website |
FAS-DPD (RRID:SCR_003068) | FAS-DPD | software resource | Software program to design degenerate primers for PCR. | command-line, java, primer, pcr, degenerate primer |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23533783 | Free, Available for download, Freely available | OMICS_02340 | SCR_003068 | family-specific degenerate primer design | 2026-09-12 12:55:51 | 0 | ||||||
|
DnaSP Resource Report Resource Website 5000+ mentions |
DnaSP (RRID:SCR_003067) | DnaSP | data analysis software, data processing software, software application, software resource | A software package for the analysis of nucleotide polymorphism from aligned DNA sequence data. DnaSP can estimate several measures of DNA sequence variation within and between populations (in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters. DnaSP can also carry out several tests of neutrality: Hudson, Kreitman and Aguad (1987), Tajima (1989), McDonald and Kreitman (1991), Fu and Li (1993), and Fu (1997) tests. Additionally, DnaSP can estimate the confidence intervals of some test-statistics by the coalescent. The results of the analyses are displayed on tabular and graphic form. | genetics, dna, population genetics, sequence, polymorphism, nucleotide polymorphism, dna sequence, population, noncoding, synonymous, nonsynonymous |
is listed by: OMICtools has parent organization: University of Barcelona; Barcelona; Spain |
Spanish Direccion General de Investigacion Cientifica y Technica PB91-0245; Spanish Direccion General de Investigacion Cientifica y Technica PB94-0923; Spanish Direccion General de Investigacion Cientifica y Technica PB97-0918; Spanish Direccion General de Investigacion Cientifica y Technica TXT98-1802; Spanish Direccion General de Investigacion Cientifica y Technica BMC2001-2906; Spanish Direccion General de Investigacion Cientifica y Technica BFU2004-02253; Spanish Direccion General de Investigacion Cientifica y Technica BFU2007-6292 |
PMID:19346325 PMID:19378153 PMID:14668244 PMID:10089204 PMID:9183537 PMID:8808578 |
Free, Available for download, Freely available | OMICS_01820, nif-0000-30461 | SCR_003067 | DNA Sequence Polymorphism | 2026-09-12 12:55:51 | 6215 | |||||
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JuncBASE Resource Report Resource Website 10+ mentions |
JuncBASE (RRID:SCR_003103) | data analysis software, data processing software, software application, software resource | Software used to identify and classify alternative splicing events from RNA-Seq data. JuncBASE also uses read counts to quantify the relative expression of each isoform and identifies splice events that are significantly differentially expressed across two or more samples. | splicing event, splicing events, alternative splicing event, rna seq |
is listed by: OMICtools is hosted by: GitHub |
Free, Available for download, Freely available | OMICS_01335 | https://github.com/anbrooks/juncBASE | SCR_003103 | 2026-09-12 12:55:51 | 19 | ||||||||
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brainmap.org Resource Report Resource Website 100+ mentions |
brainmap.org (RRID:SCR_003069) | BrainMap | data or information resource, database, software application, software resource | A community database of published functional and structural neuroimaging experiments with both metadata descriptions of experimental design and activation locations in the form of stereotactic coordinates (x,y,z) in Talairach or MNI space. BrainMap provides not only data for meta-analyses and data mining, but also distributes software and concepts for quantitative integration of neuroimaging data. The goal of BrainMap is to develop software and tools to share neuroimaging results and enable meta-analysis of studies of human brain function and structure in healthy and diseased subjects. It is a tool to rapidly retrieve and understand studies in specific research domains, such as language, memory, attention, reasoning, emotion, and perception, and to perform meta-analyses of like studies. Brainmap contains the following software: # Sleuth: database searches and Talairach coordinate plotting (this application requires a username and password) # GingerALE: performs meta-analyses via the activation likelihood estimation (ALE) method; also converts coordinates between MNI and Talairach spaces using icbm2tal # Scribe: database entry of published functional neuroimaging papers with coordinate results | 3d model, atlas, data management, imaging, map, neuroinformatics, warping, neuroimaging, brain, talairach, mni, java, modeling, magnetic resonance, nifti-1, ontology, os independent, pet, spect, visualization, functional neuroimaging, fmri |
uses: Scribe is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Brede Database has parent organization: University of Texas Health Science Center at San Antonio; Texas; USA is parent organization of: Sleuth is parent organization of: GingerALE |
Healthy, Diseased | NIMH 2R01-MH074457 | PMID:15897617 PMID:11967563 PMID:15846810 |
Free, Freely available | nif-0000-00049 | http://www.nitrc.org/projects/brainmap | SCR_003069 | BrainMap Database | 2026-09-12 12:55:51 | 484 | |||
|
pFind Resource Report Resource Website 100+ mentions |
pFind (RRID:SCR_003011) | software resource | A search engine system for automated peptide and protein identification from tandem mass spectra. | mass spectrometry, proteomics |
is listed by: OMICtools has parent organization: Chinese Academy of Sciences; Beijing; China |
PMID:17702057 | OMICS_02467 | SCR_003011 | 2026-09-12 12:55:50 | 132 | |||||||||
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AlzSWAN Knowledge Base Resource Report Resource Website 1+ mentions |
AlzSWAN Knowledge Base (RRID:SCR_003017) | AlzSWAN | community building portal, data or information resource, knowledge environment, knowledgebase, portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A community-driven knowledgebase of Alzheimer disease, in which researchers can annotate scientific claims, data, and information, putting these into the context of testable hypotheses and treatment discovery. This SWAN project adds a collection of hand-curated hypotheses to a research paper, which are then related through a set of discourse relationships. They can be browsed and relations between claims, as well as support networks for a specific claim, are made and visualized. AlzSWAN is where you explore scientific knowledge about Alzheimer disease and share your own ideas, comments and questions in a semantically structured system. AlzSWAN is enabled by Semantic Web technology, a new standard for knowledge organization and transfer on the Web. AlzSWAN organizes and manages knowledge using formal knowledge descriptions called ontologies. Using these formal knowledge descriptions, they can tie statements made in scientific publications or on the Web to scientific evidence, biological terminologies, and knowledgebases, and to claims and counterclaims made by other researchers. | hypothesis, claim, research paper, relationship, semantics, annotation |
is listed by: FORCE11 is related to: Semantic Web Applications in Neuromedicine (SWAN) Ontology has parent organization: Alzheimer's Research Forum |
Alzheimer's disease | Ellison Medical Foundation ; alz.org |
PMID:17510163 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00524 | SCR_003017 | 2026-09-12 12:55:50 | 1 | |||||
|
GenePaint Resource Report Resource Website 100+ mentions |
GenePaint (RRID:SCR_003015) | GenePaint.org | atlas, data or information resource, database, expression atlas, reference atlas | Digital atlas of gene expression patterns in developing and adult mouse. Several reference atlases are also available through this site. Expression patterns are determined by non-radioactive in situ hybridization on serial tissue sections. Sections are available from several developmental ages: E10.5, E14.5 (whole embryos), E15.5, P7 and P56 (brains only). To retrieve expression patterns, search by gene name, site of expression, GenBank accession number or sequence homology. For viewing expression patterns, GenePaint.org features virtual microscope tool that enables zooming into images down to cellular resolution. | gene expression, adult mouse, annotated, c57bl6, mouse, mouse embryo, mrna, non radioactive in situ hybridization, light microscopy, molecular neuroanatomy resource, in situ hybridization, embryonic, postnatal, adult, brain, head, annotation, rna probe, sequence, anatomical structure, FASEB list |
has parent organization: Max Planck Institute for Biophysical Chemistry; Gottingen; Germany is parent organization of: GenePaint E15 Atlas is parent organization of: GenePaint P7 Atlas is parent organization of: GenePaint P56 Mouse Atlas is parent organization of: GenePaint Interactive Anatomy Atlas |
BMBF ; Burroughs Wellcome Fund ; European Union ; Max Planck Society ; Merck Genome Research Institute ; NINDS ; Romansky Endowment |
PMID:14681479 PMID:22936000 |
nif-0000-00009, SCR_017526 | SCR_003015 | Atlas of Gene Expression Patterns in Mouse Embryo | 2026-09-12 12:55:50 | 164 | ||||||
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EUROpean Saccharomyces Cerevisiae ARchive for Functional Analysis Resource Report Resource Website 10+ mentions |
EUROpean Saccharomyces Cerevisiae ARchive for Functional Analysis (RRID:SCR_003093) | EUROSCARF | biomaterial supply resource, material resource, organism supplier | Archive of yeast strains and plasmids that were generated during various yeast functional analysis projects. | plasmid, strain, wild type, deletion, tap fusion, degron, orf, functional analysis, yeast |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Goethe University Frankfurt am Main; Hessen; Germany |
BMBF ; European UnionROFAN I and II ; European yeast industrial platform ; federal state of Hessen |
Free, Freely available | nif-0000-30504 | http://www.uni-frankfurt.de/fb15/mikro/EUROSCARF/indexhtml | SCR_003093 | 2026-09-12 12:55:51 | 43 | ||||||
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JETTA Resource Report Resource Website 1+ mentions |
JETTA (RRID:SCR_003091) | JETTA | data analysis software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented July 6, 2017. Software to detect alternatively spliced exons between two conditions, for example, between two groups of treated and untreated patients in a typical clinical study. | exon, exon splicing |
is listed by: OMICtools has parent organization: Stanford University; Stanford; California |
PMID:22433281 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01334 | SCR_003091 | 2026-09-12 12:55:51 | 3 | |||||||
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Effect Size Calculator Resource Report Resource Website 10+ mentions |
Effect Size Calculator (RRID:SCR_003094) | Effect Size Calculators | analysis service resource, data analysis service, production service resource, service resource, software resource, web application | Calculator for a variety of functions, including Cohen's d and the effect-size correlation, rYl, using means and standard deviations or independent groups t test values and df. | calculator, cohen, cohen d, ryi, effect size correlation | has parent organization: University of Colorado; Colorado Springs; USA | Free, Freely available | nif-0000-30507 | https://lbecker.uccs.edu/ | SCR_003094 | 2026-09-12 12:55:51 | 13 | |||||||
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Biomedical Information Science and Technology Initiative Resource Report Resource Website 1+ mentions |
Biomedical Information Science and Technology Initiative (RRID:SCR_003123) | BISTI | data or information resource, funding resource, meeting resource, organization portal, portal, training resource | A consortium of representatives from each of the NIH institutes and centers. BISTI was established in May 2000 to serve as the focus of biomedical computing issues at the NIH. The mission of BISTI is to make optimal use of computer science and technology to address problems in biology and medicine by fostering new basic understandings, collaborations, and transdisciplinary initiatives between the computational and biomedical sciences. In support of this mission, the BISTI coordinates research grants, training opportunities, and scientific symposia associated with biomedical computing. Regular monthly meetings are conducted to discuss program status, future needs and directions, and topics of interest to the bioinformatics community. | grant, funding opportunity, computer science, technology, biology, medicine, collaboration, transdisciplinary initiative, computation, biomedical sciences, bioinformatics, informatics | has parent organization: National Institutes of Health | NIH Blueprint for Neuroscience Research | Free, Freely available | nif-0000-00560 | https://stip.oecd.org/stip/interactive-dashboards/policy-initiatives/2021%2Fdata%2FpolicyInitiatives%2F25417 | SCR_003123 | Biomedical Information Science Technology Initiative, BITSI - Biomedical Information Science and Technology Initiative, Biomedical Information Science & Technology Initiative | 2026-09-12 12:55:52 | 1 | |||||
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BioCaster Ontology Resource Report Resource Website |
BioCaster Ontology (RRID:SCR_003122) | BCO | controlled vocabulary, data or information resource, ontology | A multilingual application ontology aimed at the early detection of public health events in the media. It aims to describe the terms and relations necessary to detect and risk assess public health events in the grey literature at an early stage; and bridge the gap between the (multilingual) grey literature and existing standards in biomedicine. The BCO focuses on the usage of terms and relations within informal unstructured reports which are often made at a pre-diagnostic stage of a disease outbreak by non-medically trained reporters. This is done to provide monitoring and early warning about public health hazards from online media reports. | public health, text-mining, infectious disease, owl, skos, database |
has parent organization: Google Code has parent organization: BioCaster |
Infectious disease | Free, Available for download, Freely available | nlx_156797 | http://born.nii.ac.jp/_dev/static/ontology | SCR_003122 | biocaster-ontology | 2026-09-12 12:55:52 | 0 | |||||
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Genetic Analysis Package Resource Report Resource Website 1+ mentions |
Genetic Analysis Package (RRID:SCR_003006) | software resource | GAP is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, classic twin models, probability of familial disease aggregation, kinship calculation, some statistics in linkage analysis, and association analysis involving one or more genetic markers including haplotype analysis with or without environmental covariates. | genetic, analysis, package, data, population, family, calculation, family, disease, aggregation, kinship, environmental, covariate, haplotype, marker | nif-0000-30271 | SCR_003006 | GAP | 2026-09-12 12:55:50 | 1 | ||||||||||
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ISPS Data Archive Resource Report Resource Website 1+ mentions |
ISPS Data Archive (RRID:SCR_003127) | ISPS Data Archive | data or information resource, data repository, data set, service resource, storage service resource | Data archive to assist in the sharing of research grade information pertaining to the social and economic sciences. The majority of digital content currently consists of social science research data from experiments, program files with the code for analyzing the data, requisite documentation to use and understand the data, and associated files. Access to the ISPS Data Archive is provided at no cost and is granted for scholarship and research purposes only. When possible, Data is linked to Projects and Publications, via the ISPS KnowledgeBase. ISPS operates in accordance with the prevailing standards and practices of the digital preservation community including the Open Archival Information System (OAIS) Reference Model (ISO 14721:2003) and the Data Documentation Initiative (DDI) standard. Accordingly, ISPS supports digital life-cycle management, interoperability, and preferred methods of preservation. The ISPS Data Archive is intended for use by social science researchers, policy-makers, and practitioners who are conducting or analyzing field (and other) experiments in various social science disciplines. Currently, Replication Files originate with ISPS-affiliated scholars. | life-cycle management, interoperability, preservation, scholarly community, scholarship, data curation, social sciences, economics, political science, political science literature, political ethics, bioethics |
is listed by: re3data.org has parent organization: Yale University; Connecticut; USA |
Free, Freely available | nlx_156779, r3d100010833 | https://doi.org/10.17616/R3FP5M | SCR_003127 | Yale University Institution for Social and Policy Studies Data Archive, Yale ISPS Data Archive | 2026-09-12 12:55:52 | 1 | ||||||
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Primer3Plus Resource Report Resource Website 1000+ mentions |
Primer3Plus (RRID:SCR_003081) | Primer3Plus | analysis service resource, data analysis service, production service resource, service resource, software resource, source code | A web interface to the Primer3 primer design program as an enhanced alternative for the CGI- scripts that come with Primer3. | primer, dna sequence, primer design, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Primer3 has parent organization: Wageningen University and Research Centre; Gelderland; Netherlands |
Howard Hughes Medical Institute ; NHGRI R01-HG00257; NHGRI P50-HG00098 |
PMID:17485472 | Free, Freely available | biotools:primer3plus, OMICS_02347 | https://bio.tools/primer3plus | SCR_003081 | Primer3Plus - pick primers from a DNA sequence | 2026-09-12 12:55:51 | 1860 | ||||
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NeuroML Resource Report Resource Website 10+ mentions |
NeuroML (RRID:SCR_003083) | NeuroML | data or information resource, interchange format, markup language, narrative resource, standard specification | A XML-based description language that provides a common data format for defining and exchanging descriptions of neuronal cell and network models. It facilitates the exchange of complex neural models, allows for greater transparency and accessibility of models, enhances interoperability between simulators and other tools, and supports the development of new software and databases. Exchange of network models will aid the investigation of structure-function relationships in neuroscience including theoretical studies relating connectivity patterns to normal and neurodegenerative network states. NeuroML is a free and open community effort developed with input from many contributors. They will need your help as the standards and tools continue to evolve. | cell, network, neuron, model, computation tool, neuronal cell, network model |
is used by: Open Source Brain is used by: CNrun is related to: GENESIS Neural Database and Modelers Workspace is related to: Neural Open Simulation is related to: ChannelDB is related to: neuroConstruct has parent organization: University College London; London; United Kingdom has parent organization: Arizona State University; Arizona; USA is parent organization of: Tools in NeuroML |
Free, Freely available | nif-0000-00542 | SCR_003083 | Neuro-Markup Language | 2026-09-12 12:55:51 | 34 | |||||||
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Japanese Genotype-phenotype Archive (JGA) Resource Report Resource Website 10+ mentions |
Japanese Genotype-phenotype Archive (JGA) (RRID:SCR_003118) | JGA | data or information resource, data repository, database, service resource, storage service resource | A service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The JGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the JGA. Once processed, all data are encrypted. The JGA accepts only de-identified data approved by JST-NBDC. The JGA implements access-granting policy whereby the decisions of who will be granted access to the data resides with the JST-NBDC. After data submission the JGA team will process the data into databases and archive the original data files. The accepted data types include manufacturer-specific raw data formats from the array-based and new sequencing platforms. The processed data such as the genotype and structural variants or any summary level statistical analyses from the original study authors are stored in databases. The JGA also accepts and distributes any phenotype data associated with the samples. For other human biological data, please contact the NBDC human data ethical committee. | biomedical, genetic, phenotype, gene, data sharing, genotype |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases has parent organization: DNA DataBank of Japan (DDBJ) has parent organization: NBDC - National Bioscience Database Center |
Free, Freely available | nlx_156741, r3d100010818 | https://doi.org/10.17616/R3861Q | http://trace.ddbj.nig.ac.jp/jga/, http://trace.ddbj.nig.ac.jp/jga/index_e.html | SCR_003118 | JGA, Japanese Genotype-phenotype Archive (JGA), Japanese Genotype-phenotype Archive | 2026-09-12 12:55:52 | 37 | |||||
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tweeDEseq Resource Report Resource Website 1+ mentions |
tweeDEseq (RRID:SCR_003038) | software resource | Software for differential expression analysis of RNA-seq using the Poisson-Tweedie family of distributions. | standalone software, unix/linux, mac os x, windows, c, r, rna-seq, differential expression, sequencing, statistical method, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23965047 | Free, Available for download, Freely available | OMICS_02406, biotools:tweedeseq | https://bio.tools/tweedeseq | SCR_003038 | tweeDEseq: RNA-seq data analysis using the Poisson-Tweedie family of distributions | 2026-09-12 12:55:50 | 4 |
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The data sets included in this resource are published in Kravitz et al, 2012. Distinct roles for direct and indirect pathway striatal neurons in reinforcement (Nat. Neurosci).
