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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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IQRray Resource Report Resource Website 1+ mentions |
IQRray (RRID:SCR_006057) | IQRray | software resource | Software based on evolutionary conservation of expression profiles, implemented in R, for identification of poor quality arrays in dataset composed of arrays from many independent experiments. | r, affymetrix, microarray, quality control, evolutionary conservation, expression profile, probe |
is listed by: OMICtools has parent organization: University of Lausanne; Lausanne; Switzerland |
PMID:24451627 | Free, Public | OMICS_02244 | SCR_006057 | SciCrunch Registry | 2026-09-26 02:13:59 | 2 | |||||||
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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 | 2026-09-26 02:14:00 | 5 | ||||||
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WashU Epigenome Browser Resource Report Resource Website 100+ mentions |
WashU Epigenome Browser (RRID:SCR_006208) | Human Epigenome Browser | data analysis software, data or information resource, data processing software, data set, software application, software resource, source code | Software tool for visualizing and interacting with whole-genome datasets. Browser hosts Human Epigenome Atlas data produced by Roadmap Epigenomics project, but its use of advanced, multi-resolution data formats and its user-friendly interface make it possible for investigators to upload and visualize their own data as custom tracks. Developed and maintained by Epigenome Informatics Group at Washington University in St. Louis. | epigenomics, genome browser, visualization, clustering, genome, sequencing, next-generation sequencing, virus |
is listed by: OMICtools is related to: VizHub is related to: UCSC Genome Browser is related to: Human Epigenome Atlas has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA has parent organization: Roadmap Epigenomics Project |
PMID:22127213 | Free, Freely available | OMICS_00629, nlx_151754 | http://epigenomegateway.wustl.edu/browser/ | SCR_006208 | SciCrunch Registry | WashU Epigenome Browser, WashU Genome Browser, Human Epigenome Browser at Washington University | 2026-09-26 02:14:01 | 184 | |||||
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InterSpecies Analysing Application using Containers Resource Report Resource Website 10+ mentions |
InterSpecies Analysing Application using Containers (RRID:SCR_006243) | ISAAC | analysis service resource, data analysis service, production service resource, service resource, software resource | Web based tool to enable the analysis of sets of genes, transcripts and proteins under different biological viewpoints and to interactively modify these sets at any point of the analysis. Detailed history and snapshot information allows tracing each action. One can switch back to previous states and perform new analyses. Sets can be viewed in the context of genomes, protein functions, protein interactions, pathways, regulation, diseases and drugs. Additionally, users can switch between species with an automatic, orthology based translation of existing gene sets. Sets as well as results of analyses can be exchanged between members of groups. | protein function, protein interaction, pathway, mirna, disease, drug, gene, genome, transcript, protein, regulation |
is listed by: OMICtools is related to: Gene Ontology has parent organization: University of Wurzburg; Bavaria; Germany |
PMID:24428905 | OMICS_02237 | SCR_006243 | SciCrunch Registry | ISAAC (Interspecies Analysing Application using Containers), ISAAC - InterSpecies Analysing Application using Containers, Interspecies Analysing Application using Containers - ISAAC | 2026-09-26 02:14:01 | 37 | |||||||
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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 | 2026-09-26 02:14:01 | 481 | |||||||
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YuGene Resource Report Resource Website 10+ mentions |
YuGene (RRID:SCR_006023) | software resource | Software providing a simple method for comparison of gene expression generated across different experiments, and on different platforms; that does not require global renormalization, and is not restricted to comparison of identical probes. YuGene works on a range of microarray dataset distributions, such as between manufacturers. The resulting output allows direct comparisons of gene expression between experiments and experimental platforms. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:24667244 | GNU General Public License, v2, v3 | OMICS_04030 | SCR_006023 | SciCrunch Registry | YuGene: A simple approach to scale gene expression data derived from different platforms for integrated analyses | 2026-09-26 02:13:59 | 16 | |||||||
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GNUMAP-BS Resource Report Resource Website 1+ mentions |
GNUMAP-BS (RRID:SCR_005995) | GNUMAP-BS | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 3rd,2023. A probabilistic algorithm that addresses the computational problems associated with aligning bisulfite sequencing data to a reference genome. |
is listed by: OMICtools has parent organization: Brigham Young University; Utah; USA |
PMID:24261665 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00583 | SCR_005995 | SciCrunch Registry | 2026-09-26 02:13:58 | 2 | ||||||||
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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 | 2026-09-26 02:14:02 | 6255 | ||||
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h5vc Resource Report Resource Website 1+ mentions |
h5vc (RRID:SCR_006039) | h5vc | software resource | Software package that contains functions to interact with tally data from Next-Generation Sequencing (NGS) experiments that is stored in HDF5 files. | next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: European Bioinformatics Institute |
PMID:24451629 | GNU General Public License, v3 or newer | biotools:h5vc, OMICS_02243 | http://www.ebi.ac.uk/~pyl/h5vc/, https://bio.tools/h5vc | SCR_006039 | SciCrunch Registry | h5vc - Scalable nucleotide tallies with HDF5, h5vc - Managing alignment tallies using a hdf5 backend | 2026-09-26 02:13:59 | 2 | |||||
|
CAFE Resource Report Resource Website 500+ mentions |
CAFE (RRID:SCR_005983) | CAFE | software resource | R software package for the detection of gross chromosomal abnormalities from gene expression microarray data. | affymetrix, r, chromosomal abnormality, gene expression, microarray, chromosome, linux, windows |
is listed by: OMICtools has parent organization: Bitbucket |
PMID:24451624 | GNU General Public License, v3, Acknowledgement requested | OMICS_02245 | SCR_005983 | SciCrunch Registry | 2026-09-26 02:13:58 | 883 | |||||||
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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 | 2026-09-26 02:14:01 | 32 | |||||||
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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 | 2026-09-26 02:14:03 | 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 | 2026-09-26 02:14:03 | 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 | 2026-09-26 02:14:03 | 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 | 2026-09-26 02:14:03 | 0 | |||||||
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SAAP-RRBS Resource Report Resource Website 10+ mentions |
SAAP-RRBS (RRID:SCR_006516) | SAAP-RRBS | software resource | Streamlined Analysis and Annotation Pipeline for reduced representation bisulfite sequencing. | genomics, next generation sequencing |
is listed by: OMICtools has parent organization: Google Code |
GNU General Public License, v3, Acknowledgement requested | OMICS_00612 | SCR_006516 | SciCrunch Registry | Streamlined Analysis and Annotation Pipeline for reduced representation bisulfite sequencing | 2026-09-26 02:14:05 | 10 | |||||||
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European Nucleotide Archive (ENA) Resource Report Resource Website 1000+ mentions |
European Nucleotide Archive (ENA) (RRID:SCR_006515) | ENA | data or information resource, data repository, database, service resource, storage service resource | Public archive providing a comprehensive record of the world''''s nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. All submitted data, once public, will be exchanged with the NCBI and DDBJ as part of the INSDC data exchange agreement. The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. ENA records this information in a data model that covers input information (sample, experimental setup, machine configuration), output machine data (sequence traces, reads and quality scores) and interpreted information (assembly, mapping, functional annotation). Data arrive at ENA from a variety of sources including submissions of raw data, assembled sequences and annotation from small-scale sequencing efforts, data provision from the major European sequencing centers and routine and comprehensive exchange with their partners in the International Nucleotide Sequence Database Collaboration (INSDC). Provision of nucleotide sequence data to ENA or its INSDC partners has become a central and mandatory step in the dissemination of research findings to the scientific community. ENA works with publishers of scientific literature and funding bodies to ensure compliance with these principles and to provide optimal submission systems and data access tools that work seamlessly with the published literature. ENA is made up of a number of distinct databases that includes the EMBL Nucleotide Sequence Database (Embl-Bank), the newly established Sequence Read Archive (SRA) and the Trace Archive. The main tool for downloading ENA data is the ENA Browser, which is available through REST URLs for easy programmatic use. All ENA data are available through the ENA Browser. Note: EMBL Nucleotide Sequence Database (EMBL-Bank) is entirely included within this resource. | analysis, bioinformatics, dna, nucleotide, sequencing, web service, rna, molecular biology, nucleotide sequence, protein, gene expression, gene, genome, biochemistry, molecular structure, metabolite, protein binding, chemogenomics, gold standard |
is used by: BioSample Database at EBI is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: 3DVC is listed by: re3data.org is listed by: OMICtools is related to: NCBI Sequence Read Archive (SRA) is related to: ENA Sequence Version Archive is related to: VBASE2 is related to: DDBJ Sequence Read Archive is related to: ISA Infrastructure for Managing Experimental Metadata is related to: DNA DataBank of Japan (DDBJ) is related to: DNA DataBank of Japan (DDBJ) is related to: NCBI is related to: INSDC is related to: INSDC is related to: NCBI Assembly Archive Viewer has parent organization: European Bioinformatics Institute is parent organization of: ENA Sequence Search works with: Eutherian comparative genomic analysis protocol |
EMBL ; Wellcome Trust ; European Union |
PMID:20972220 | Public, The community can contribute to this resource, Acknowledgement requested | OMICS_01029, r3d100010527, nif-0000-32981 | http://www.ebi.ac.uk/embl/, https://doi.org/10.17616/R3HW3J | SCR_006515 | SciCrunch Registry | ENA, European Nucleotide Archive | 2026-09-26 02:14:05 | 1344 | ||||
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IRanges Resource Report Resource Website 50+ mentions |
IRanges (RRID:SCR_006420) | IRanges | software resource | Software tool for computing and annotating genomic ranges.Provides efficient low-level and highly reusable S4 classes for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more generally, data that can be organized sequentially (formally defined as Vector objects), as well as views on these Vector objects. Efficient list-like classes are also provided for storing big collections of instances of the basic classes. All classes in the package use consistent naming and share the same rich and consistent Vector API as much as possible. | Annotating genomic ranges, computing genomic ranges, genomic ranges, storing ranges of integers, bio.tools |
is used by: riboWaltz is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:23950696 | Free, Available for download, Freely available | OMICS_01163, biotools:iranges | https://bio.tools/iranges | SCR_006420 | SciCrunch Registry | Infrastructure for manipulating intervals on sequences | 2026-09-26 02:14:04 | 88 | |||||
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VICUNA Resource Report Resource Website 10+ mentions |
VICUNA (RRID:SCR_006302) | VICUNA | software resource | A de novo assembly program targeting populations with high mutation rates. | c++, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Broad Institute |
PMID:22974120 | biotools:vicuna, OMICS_02162 | https://bio.tools/vicuna | SCR_006302 | SciCrunch Registry | 2026-09-26 02:14:02 | 26 | |||||||
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ART Resource Report Resource Website 1+ mentions |
ART (RRID:SCR_006538) | ART | software resource | A set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms: Illumina''''s Solexa, Roche''''s 454 and Applied Biosystems'''' SOLiD. ART can be used to test or benchmark a variety of method or tools for next-generation sequencing data analysis, including read alignment, de novo assembly, SNP and structure variation discovery. ART is implemented in C++ with optimized algorithms and is highly efficient in read simulation. ART outputs reads in the FASTQ format, and alignments in the ALN format. ART can also generate alignments in the SAM alignment or UCSC BED file format. | next-generation sequencing |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite is related to: 1000 Genomes: A Deep Catalog of Human Genetic Variation has parent organization: National Institute of Environmental Health Sciences |
PMID:22199392 DOI:10.1093/bioinformatics/btr708 |
Free, Public | OMICS_00247 | https://sources.debian.org/src/augustus/ | SCR_006538 | SciCrunch Registry | ART - Set of Simulation Tools | 2026-09-26 02:14:06 | 9 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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