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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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FCROS Resource Report Resource Website 1+ mentions |
FCROS (RRID:SCR_006195) | FCROS | software resource | A fold change ranks ordering statistics based software for detecting differentially expressed genes. | differentially expressed, gene, fold, statistics, windows, os x, microarray | is listed by: OMICtools | PMID:24423217 | GNU General Public License, v2, v3 | OMICS_02234 | SCR_006195 | SciCrunch Registry | fold change rank ordering statistics, fcros: FCROS for detecting differentially expressed genes | 2026-10-17 01:26:32 | 5 | ||||||
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RUVSeq Resource Report Resource Website 100+ mentions |
RUVSeq (RRID:SCR_006263) | software resource | Software package that implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. | software package, unix/linux, mac os x, windows, r, differential expression, preprocessing, rna-seq |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:25150836 | Artistic License, v2 | OMICS_05652 | SCR_006263 | SciCrunch Registry | RUVSeq: Remove Unwanted Variation from RNA-Seq Data | 2026-10-17 01:26:29 | 481 | |||||||
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Galaxy Resource Report Resource Website 5000+ mentions |
Galaxy (RRID:SCR_006281) | Galaxy | analysis service resource, data analysis service, data or information resource, organization portal, portal, production service resource, service resource | Open, web-based platform providing bioinformatics tools and services for data intensive genomic research. Platform may be used as a service or installed locally to perform, reproduce, and share complete analyses. Galaxy automatically tracks and manages data provenance and provides support for capturing the context and intent of computational methods. Galaxy Community has created Galaxy instances in many different forms and for many different applications including Galaxy servers, cloud services that support Galaxy instances, and virtual machines and containers that can be easily deployed for your own server.The Galaxy team is a part of BX at Penn State, and the Biology and Mathematics and Computer Science departments at Emory University.Training Infrastructure as a Service (TIaaS) is a service offered by some UseGalaxy servers to specifically support training use cases. | bioinformatics, workflow, analysis, data sharing, visualization, cloud, genomics, metagenomics, next-generation sequencing, platform, data set, genaddiction tool |
is used by: Nebula lists: PathwayMatcher is listed by: OMICtools is listed by: 3DVC is listed by: Debian is listed by: SoftCite is related to: ABrowse is related to: TRAMS is related to: Stem Cell Commons is related to: Stem Cell Discovery Engine is related to: CardioVascular Research Grid (CVRG) is related to: rQuant is related to: SnpEff is related to: Binding and Expression Target Analysis is related to: PIPE-CLIP is related to: Stem Cell Discovery Engine is related to: Computational Genomics Analysis Tools is related to: SpliceTrap is related to: SMAGEXP is related to: CandiMeth is related to: ewas-galaxy is related to: CLIP-Explorer is related to: Galactic Circos is related to: Tool recommender system in Galaxy is related to: NanoGalaxy is related to: Cistrome is related to: Training Infrastructure as a Service has parent organization: Pennsylvania State University is parent organization of: kmer-SVM works with: Deeptools |
Huck Institutes for the Life Sciences ; Institute for CyberScience at Pennsylvania State University ; Pennsylvania ; USA ; Johns Hopkins University ; NHGRI HG004909; NHGRI HG005133; NHGRI HG005542; NSF DBI0850103; Pennsylvania Department of Health |
PMID:20738864 PMID:20069535 PMID:16169926 |
Free, Freely available | nlx_151896, OMICS_01141 | https://usegalaxy.org/, https://sources.debian.org/src/galaxy/ | SCR_006281 | SciCrunch Registry | The Galaxy Project, Galaxy Project | 2026-10-17 01:26:38 | 6255 | ||||
|
Genomic Standards Consortium Resource Report Resource Website 10+ mentions |
Genomic Standards Consortium (RRID:SCR_006273) | GSC | data or information resource, international standard specification, knowledge environment, narrative resource, standard specification | An open-membership International community to promote mechanisms that standardize the description of genomes and the exchange and integration of genomic data. Community-driven standards have the best chance of success if developed within the auspices of international working groups. Participants in the GSC include biologists, computer scientists, those building genomic databases and conducting large-scale comparative genomic analyses, and those with experience of building community-based standards. The mission of the GSC is to work with the wider community towards: * the implementation of new genomic standards * methods of capturing and exchanging metadata * harmonization of metadata collection and analysis efforts across the wider genomics community | genome, genomics, standards |
is listed by: OMICtools is related to: Minimum Information for Biological and Biomedical Investigations is related to: FAIRsharing is related to: Ontology for Biomedical Investigations is related to: OBO is related to: ISA Infrastructure for Managing Experimental Metadata is parent organization of: Gazetteer |
National Institute for Environmental eScience ; NERC NE/3521773/1 |
nlx_151884, OMICS_01780 | http://gensc.org/gc_wiki/index.php/Main_Page | SCR_006273 | SciCrunch Registry | 2026-10-17 01:26:31 | 32 | |||||||
|
MEGA-MD Resource Report Resource Website |
MEGA-MD (RRID:SCR_006403) | MEGA-MD | analysis service resource, data analysis service, production service resource, service resource, software resource | Software to forecast the deleteriousness of non-synonymous single nucleotide variants (nsSNVs) using multiple methods and explore them in the context of the variability permitted in the long-term evolution of the affected positions. A web version (MEGA-MDW) is also available. | windows, non-synonymous single nucleotide variant | is listed by: OMICtools | PMID:24413669 | Free for academic use, Registration required, Acknowledgement requested | OMICS_02211 | SCR_006403 | SciCrunch Registry | Molecular Evolutionary Genetics Analysis - Mutation Diagnosis, Molecular Evolutionary Genetics Analysis software with mutational diagnosis | 2026-10-17 01:26:34 | 0 | ||||||
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CGARS Resource Report Resource Website |
CGARS (RRID:SCR_006404) | CGARS | software resource | Software package to dissect random from non-random patterns in copy number data and thereby to assess significantly enriched somatic copy number aberrations (SCNA) across a set of tumor specimens or cell lines. | genome, analysis |
is listed by: OMICtools has parent organization: University of Cologne; Cologne; Germany |
Cancer | PMID:24413525 | GNU General Public License, v3 or later | OMICS_02210 | SCR_006404 | SciCrunch Registry | CGARS: Cancer Genome Analysis by Rank Sums, Cancer Genome Analysis by Rank Sums | 2026-10-17 01:26:41 | 0 | |||||
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Wigwams Resource Report Resource Website 1+ mentions |
Wigwams (RRID:SCR_006400) | Wigwams | software resource | A computational tool for analyzing multiple gene expression time series data sets for the same organism. The goal is to determine if there is evidence for gene regulatory mechanisms that are shared by multiple different expression responses. | matlab, gene, gene module, co-regulation, time series, gene expression, differential expression |
is listed by: OMICtools has parent organization: University of Warwick; Coventry; United Kingdom |
PMID:24351708 | OMICS_02214 | SCR_006400 | SciCrunch Registry | 2026-10-17 01:26:41 | 1 | ||||||||
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BETASEQ Resource Report Resource Website |
BETASEQ (RRID:SCR_006401) | BETASEQ | software resource | Software to control Type-I error inflation in partially sequenced data for rare variant association testing. It is typically used to combine sequence and genotype data for the two stage design, in which individuals sequenced in stage one for variant detection are solely or predominantly cases then in stage two the discovered variants are genotyped in the remaining individuals. BETASEQ can work with any existing rare variant association methods that use genotypes or imputed genotypes as input. | variant association testing, variant association, variant |
is listed by: OMICtools has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:24336643 | Free, Public | OMICS_02213 | SCR_006401 | SciCrunch Registry | 2026-10-17 01:26:33 | 0 | |||||||
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Gene Set Enrichment Analysis Resource Report Resource Website 10000+ mentions |
Gene Set Enrichment Analysis (RRID:SCR_003199) | GSEA | data analysis software, data processing software, software application, software resource, software toolkit | Software package for interpreting gene expression data. Used for interpretation of a large-scale experiment by identifying pathways and processes. | gene, expression, profile, pathway, data, set, phenotype, genome, enrichment, RNA, analysis, bio.tools, bio.tools |
is used by: Molecular Signatures Database is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: GoMapMan has parent organization: Broad Institute |
NCI ; NIGMS ; NIH |
PMID:16199517 | Free, Freely available | SCR_016882, nif-0000-30629, biotools:gsea, OMICS_02279 | http://www.broad.mit.edu/gsea, https://bio.tools/gsea | SCR_003199 | SciCrunch Registry | GSEA, Gene Set Enrichment Analysis, Gene Set Enrichment Analysis (GSEA) | 2026-10-17 01:25:47 | 20985 | ||||
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r3Cseq Resource Report Resource Website 10+ mentions |
r3Cseq (RRID:SCR_003198) | r3Cseq | data analysis software, data processing software, software application, software resource | An R/Bioconductor package to identify chromosomal interaction regions generated by chromosome conformation capture (3C) coupled to next-generation sequencing (NGS), a technique termed 3C-seq. It performs data analysis for a number of different experimental designs, as it can analyze 3C-seq data with or without a control experiment and it can be used to facilitate data analysis for experiments with multiple replicates. The r3Cseq package provides functions to perform data normalization, statistical analysis for cis/trans interactions and visualization in order to help scientists identify genomic regions that physically interact with the given viewpoints of interest. This tool greatly facilitates hypothesis generation and the interpretation of experimental results. | next-generation sequencing, genomic, interaction, chromosome conformation capture, chromosome, 3c-seq, r |
is listed by: OMICtools has parent organization: University of Bergen; Bergen; Norway has parent organization: Bioconductor |
PMID:23671339 | Free, Freely available | OMICS_01560 | SCR_003198 | SciCrunch Registry | 2026-10-17 01:25:26 | 24 | |||||||
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Stacks Resource Report Resource Website 500+ mentions |
Stacks (RRID:SCR_003184) | Stacks | data analysis software, data processing software, software application, software resource | A software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. It was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. | population genomics, genetic map, phylogenetics, genetics, next-generation sequencing, rad-seq, genotype-by-sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Oregon; Oregon; USA |
PMID:23701397 PMID:22384329 DOI:10.1111/mec.12354 |
Free, Available for download, Freely available | OMICS_01567, biotools:stacks | https://bio.tools/stacks, https://sources.debian.org/src/stacks/ | SCR_003184 | SciCrunch Registry | 2026-10-17 01:25:26 | 671 | ||||||
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RNAhybrid Resource Report Resource Website 500+ mentions |
RNAhybrid (RRID:SCR_003252) | RNAhybrid | analysis service resource, data analysis service, production service resource, service resource, software resource | Software tool for finding the minimum free energy hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode, i.e., the short sequence is hybridized to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction. | microrna, target prediction, free energy, rna, bio.tools |
is listed by: OMICtools is listed by: 3DVC is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Bielefeld University; North Rhine-Westphalia; Germany |
PMID:15383676 DOI:10.1261/rna.5248604 |
Free, Available for download, Freely available | OMICS_00416, biotools:rnahybrid, nif-0000-31412 | https://bio.tools/rnahybrid, https://sources.debian.org/src/rnahybrid/ | SCR_003252 | SciCrunch Registry | 2026-10-17 01:25:48 | 517 | ||||||
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PlantLoc Resource Report Resource Website 1+ mentions |
PlantLoc (RRID:SCR_003138) | PlantLoc | analysis service resource, data analysis service, production service resource, service resource, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023. An accurate web server for predicting plant protein subcellular localization by substantiality motif. | subcellular localization, protein |
is listed by: OMICtools has parent organization: Tongji University; Shanghai; China |
PMID:23729470 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01632 | SCR_003138 | SciCrunch Registry | PlantLoc: Plant Proteins Subcellular Localization Prediction Server | 2026-10-17 01:25:26 | 4 | ||||||
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Assembly Based ReAligner Resource Report Resource Website 10+ mentions |
Assembly Based ReAligner (RRID:SCR_003277) | ABRA | software resource | Software that is a realigner for next generation sequencing data. It uses localized assembly and global realignment to align reads more accurately, thus improving downstream analysis (detection of indels and complex variants in particular). | standalone software, c, c++, java, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24907369 | Free, Available for download, Freely available | OMICS_04668, biotools:abra | https://bio.tools/abra | SCR_003277 | SciCrunch Registry | ABRA - Assembly Based ReAligner | 2026-10-17 01:25:28 | 10 | |||||
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MetaLocGramN Resource Report Resource Website 1+ mentions |
MetaLocGramN (RRID:SCR_003154) | MetaLocGramN | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.A tool for subcellular localization prediction of Gram-negative proteins. You can also use MetaGramLocN via SOAP. SOAP enables you to invoke our method from scripts written in your programming language of choice. | subcellular localization, protein, prediction, sequence, analysis, gram-negative protein, gram-negative, gram-negative bacteria |
is listed by: OMICtools is related to: Biocatalogue - The Life Science Web Services Registry has parent organization: International Institute of Molecular and Cell Biology; Warsaw; Poland |
PMID:22705560 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01626 | SCR_003154 | SciCrunch Registry | 2026-10-17 01:25:26 | 3 | |||||||
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GeneCruiser Resource Report Resource Website 1+ mentions |
GeneCruiser (RRID:SCR_003153) | GeneCruiser | data access protocol, service resource, software resource, web service | A web service and web application for the annotation of microarray data providing integrated access to genomic information freely available from public data sources. | gene, genetic variation, probe, variation, annotation |
is listed by: OMICtools is related to: Gene Ontology has parent organization: Broad Institute |
PMID:16030072 | Free, Freely available | OMICS_00760 | https://www.broadinstitute.org/publications/broad3691 | SCR_003153 | SciCrunch Registry | 2026-10-17 01:25:47 | 4 | ||||||
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HUPO Proteomics Standards Initiative Resource Report Resource Website 10+ mentions |
HUPO Proteomics Standards Initiative (RRID:SCR_003158) | HUPO PSI | controlled vocabulary, data or information resource, knowledge environment, meeting resource, narrative resource, ontology, standard specification, training resource | Initiative to define community standards for data representation in proteomics to facilitate data comparison, exchange and verification. The main organizational unit is the work group, with a Gel Electrophoresis (GEL) work group, a Mass Spectrometry (MS) work group, a Molecular Interactions (MI) work group, a Protein Modifications (MOD) work group, a Proteomics Informatics (PI) work group, and a Sample Processing (SP) work group. The Gel Electrophoresis (GEL) work group aims to develop reporting requirements that supplement the Minimum Information About a Proteomics Experiment (MIAPE) parent document, describing the minimum information that should be reported about gel-based experimental techniques used in proteomics. The group will also develop data formats for capturing MIAPE-compliant data about gel electrophoresis and informatics performed on gel images. The Mass Spectrometry Standards Working Group defines community data formats and controlled vocabulary terms facilitating data exchange and archiving in the field of proteomics mass spectrometry. A past achievement is the mzData standard, which captures mass spectrometry output data. mzData's aim is to unite the large number of current formats (pkl's, dta's, mgf's, .....) into a single format. mzData has been released but is now deprecated in favor of mzML. The Molecular Interactions workgroup is concentrating on improving the annotation and representation of molecular interaction data wherever it is published, be this in journal articles, authors web-sites or public domain databases; and improving the accessibility of molecular interaction data to the user community. By using a common standard data can be downloaded from multiple sources and easily combined using a single parser. The protein modification workgroup focuses on developing a consensus nomenclature and provide an ontology reconciling in a hierarchical representation the complementary descriptions of residue modifications. The protein modification ontology (PSI-MOD) is available in OBO format or in OBO.xml. A spreadsheet containing the mapping of the descriptive labels used in various databases and search engines, the consensus list of proposed short name for protein modifications established by collaborative effort of mass spectrometry community, and the proposed rules and recommendations for this nomenclature are available. These short names are included in the ontology as synonyms of the corresponding terms. The Proteomics Informatics Standards Group (PSI-PI) goals are to provide a set of minimal reporting requirements which augment the MIAPE reporting guidelines with respect to analysis of data derived from proteomics experiments; to provide vendor-neutral and standard formats for representing results of analyzing and processing experimental data; to foster adoption of the format by highlighting efforts made by vendors and individuals that utilize the format in their products. The remit of the Sample Processing Working Group is to produce reporting guidelines, data exchange formats and controlled vocabulary covering all separation techniques not considered to be "classical" one- or two-dimensional gel electrophoresis (cf. the Gel WG home page), along with other kinds of sample handling and processing (for example, "tagging" proteins or peptides, splitting, combining and storing samples). Where possible we seek to develop our products in collaboration with all proteomics stakeholders and, where relevant, developers from other standards communities, most notably metabolomics. * Minimum reporting requirements: The evolving Minimum Information About a Proteomics Experiment (MIAPE) documents offer guidelines on how to adequately report a proteomics experiment. It is expected that these documents will be published, and that the requirements within will be enforced by journals, compliant repositories and funders (cf. MIAME). * XML formats for data exchange: Derived from the FuGE general object model, the formats developed by this workgroup are designed to function both as standalone files and as part of a "parent" FuGE-ML document. These formats will facilitate data exchange between researchers, and submission to repositories or journals. * Controlled vocabularies (CVs) and ontology: Lists of clearly defined terms are crucial for the construction of unambiguously worded data files. In addition to providing supporting CVs for the individual data capture formats as part of the integrated PSI CV, the Sample Processing WG will contribute terms to the Functional Genomics Ontology (FuGO). | proteomics, work group, gel electrophoresis, mass spectrometry, molecular interaction, protein modification, proteomics informatics, sample processing, controlled vocabulary, miape, transcriptome, metabolome, proteome, metadata, mass spectrometry informatics, community standards, annotation system, protein-protein interaction, protein, data format, annotation, minimal reporting requirement, nomenclature, reporting guideline, data exchange format, ontology development, rdf development, FASEB list |
is listed by: OMICtools is related to: Proteomics Identifications (PRIDE) has parent organization: HUPO - Human Proteome Organisation is parent organization of: Mass Spectrometry Ontology is parent organization of: mzML is parent organization of: PSICQUIC Registry is parent organization of: Protein-Protein Interaction Ontology is parent organization of: Sample Processing and Separation Techniques Ontology |
Free, Freely available | nif-0000-00568, OMICS_01781 | SCR_003158 | SciCrunch Registry | The HUPO Proteomics Standards Initiative | 2026-10-17 01:25:46 | 46 | |||||||
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SpliCQ Resource Report Resource Website |
SpliCQ (RRID:SCR_003266) | SpliCQ | software resource | A Java software package which allows for the identification of splicing events and differentially expressed isoforms in next generation sequencing data. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_01341 | SCR_003266 | SciCrunch Registry | 2026-10-17 01:25:49 | 0 | ||||||||
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Geospiza Resource Report Resource Website 100+ mentions |
Geospiza (RRID:SCR_003264) | Geospiza | commercial organization, material service resource, production service resource, service resource, software resource | Developer of enterprise-class software systems for workflow management of genetic analysis. Geospiza has established itself as the life science industry's top software developer for meeting the combined laboratory, data management and analytical needs of biotechnology and pharmaceutical companies, universities, researchers, contract core and diagnostic laboratories involved in genetic testing and manufacturing bio-therapeutics. Geospiza's products are designed and built by biologists, enabling researchers to focus on the science, not the software. *GeneSifter Analysis Edition: Access easy-to-use statistical, visualization and annotation tools for Microarray and Next Generation Sequencing data. *GeneSifter Lab Edition: Manage cross-platform core lab operations from a single interface out-of-the-box. | genetic analysis, microarray, next generation sequencing, data management |
is listed by: OMICtools is parent organization of: FinchTV |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01127, nif-0000-31431 | http://www.geospiza.com/finchtv.html | SCR_003264 | SciCrunch Registry | Geospiza Inc. | 2026-10-17 01:25:28 | 130 | ||||||
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ORFprimer Resource Report Resource Website 1+ mentions |
ORFprimer (RRID:SCR_003269) | ORFprimer | software resource | An extended software package for high throughput PCR primer design for biological sequences. It reads the NCBI GenBank XML sequence format and extracts open reading frames for proteins. Sequences can be requested by GI or accession number. | java, java swing, open reading frame, protein, high throughput sequencing, primer, primer design, pcr, pcr primer design |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_02331 | SCR_003269 | SciCrunch Registry | ORFprimer - primer design for ORFs | 2026-10-17 01:25:28 | 1 |
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