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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CANGS Resource Report Resource Website 1+ mentions |
CANGS (RRID:SCR_011837) | CANGS | software resource, data processing software, software application, data analysis software | A user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies. | windows, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
PMID:20180949 | biotools:cangs, OMICS_01084 | https://bio.tools/cangs | SCR_011837 | 2026-08-05 10:45:37 | 1 | |||||||
|
GeneTack Resource Report Resource Website 1+ mentions |
GeneTack (RRID:SCR_011953) | GeneTack | data or information resource, database, data analysis service, production service resource, service resource, analysis service resource | Tools for frameshift prediction and a frameshift database. | genomic sequence, transcript sequence, sequence, metagenomic sequence, frameshift |
is listed by: OMICtools has parent organization: Georgia Institute of Technology; Georgia; USA |
OMICS_01540 | SCR_011953 | GeneTack: tools for frameshift prediction | 2026-08-05 10:45:38 | 1 | ||||||||
|
JiffyNet Resource Report Resource Website 1+ mentions |
JiffyNet (RRID:SCR_011954) | software application, simulation software, software resource, data analysis service, production service resource, service resource, analysis service resource | Web based instant protein network modeler for newly sequenced species. Web server designed to instantly construct genome scale protein networks using protein sequence data. Provides network visualization, analysis pages and solution for instant network modeling of newly sequenced species. | protein network, protein, network, genome, sequence, pathway annotation, network visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Yonsei University; Seoul; South Korea |
National Research Foundation of Korea ; Next-Generation BioGreen 21 Program |
PMID:23685435 | Free, Freely available | OMICS_01548, biotools:jiffynet | https://bio.tools/jiffynet | SCR_011954 | 2026-08-05 10:45:38 | 1 | ||||||
|
BioSpace Resource Report Resource Website 100+ mentions |
BioSpace (RRID:SCR_012010) | BioSpace | data or information resource, narrative resource, job resource | Online community for industry news and careers for life science professionals. | biotechnology, pharmaceutical, career, clinical, academic, biomedical, medical device | is listed by: OMICtools | The community can contribute to this resource | OMICS_01828 | SCR_012010 | 2026-08-05 10:45:39 | 498 | ||||||||
|
sabre Resource Report Resource Website 100+ mentions |
sabre (RRID:SCR_011843) | sabre | software resource, data processing software, software application, data analysis software | Software tool to demultiplex barcoded reads into separate files. Works on both single-end and paired-end data in fastq format. Used in next generation sequencing to analyze a broad range of data. | demultiplex, bardcode, separate, fastq, format, data, next, generation, sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:sabre, OMICS_01090 | https://bio.tools/sabre | SCR_011843 | Systems Approach to Biomarker Research | 2026-08-05 10:45:37 | 199 | ||||||
|
TFClass Resource Report Resource Website 10+ mentions |
TFClass (RRID:SCR_012018) | TFClass | data or information resource, ontology, database, controlled vocabulary | Database that classifies human transcription factors based on the characteristics of their DNA-binding domains. It comprises six levels (superclasses, classes, families, subfamilies, genera and factor species), two of which are optional (subfamilies and factor species). The full classification can also be obtained as html document and as ontology in obo-format., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | transcription factor, dna-binding domain, obo | is listed by: OMICtools | BMBF ; European Union FP7 LipidomicNet 202272; European Union FP7 SysCol 258236; DFG FKZ0315890B |
PMID:23180794 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01864 | SCR_012018 | Classification of Human Transcription Factors | 2026-08-05 10:45:39 | 13 | |||||
|
TagCleaner Resource Report Resource Website 50+ mentions |
TagCleaner (RRID:SCR_011846) | software resource, software application, standalone software, web application | A software tool which can automatically detect and efficiently remove tag sequences from genomic and metagenomic datasets. | tag sequence, standalone software, web application, microbiome, genomic, metagenomic, datasets |
is listed by: OMICtools is listed by: Human Microbiome Project has parent organization: SourceForge |
Available for download | OMICS_01094 | SCR_011846 | 2026-08-05 10:45:37 | 63 | |||||||||
|
INSDC Resource Report Resource Website 100+ mentions |
INSDC (RRID:SCR_011967) | INSDC | community building portal, data or information resource, portal | International collaboration of the International Nucleotide Sequence Databases (INSD), DDBJ, ENA, and GenBank, maintained for over 18 years. Individuals submitting data to the international sequence databases should be aware of INSDC policy. | nucleotide sequence, FASEB list |
is listed by: OMICtools is affiliated with: DDBJ Sequence Read Archive is related to: DNA DataBank of Japan (DDBJ) is related to: RefSeq is related to: NCBI BioProject is related to: DNA DataBank of Japan (DDBJ) is related to: GenBank is related to: European Nucleotide Archive (ENA) is related to: GenBank is related to: European Nucleotide Archive (ENA) is related to: RefSeq is related to: UniProt Proteomes |
OMICS_01653 | SCR_011967 | International Nucleotide Sequence Database Collaboration | 2026-08-05 10:45:38 | 214 | ||||||||
|
Multivariate Analysis of Transcript Splicing Resource Report Resource Website 100+ mentions |
Multivariate Analysis of Transcript Splicing (RRID:SCR_013049) | MATS | software resource, data processing software, software application, data analysis software | Software tool to detect differential alternative splicing events from RNA-Seq data. Calculates P value and false discovery rate that difference in isoform ratio of gene between two conditions exceeds given user defined threshold. Can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. Handles replicate RNA-Seq data from both paired and unpaired study design. | Differential alternative splicing events, splicing events calculation, RNA-Seq data, gene isoform ratio, alternative splicing patterns, patterns detection, patterns analysis, replicate RNA-Seq data |
is listed by: OMICtools is listed by: SourceForge has parent organization: Childrens Hospital of Philadelphia - Research Institute; Pennsylvania; USA |
Free, Available for download, Freely available | OMICS_01336, SCR_020941 | SCR_013049 | RNAseq MATS, RMATS, rMATS, MATS, RNA MATS | 2026-08-05 10:45:56 | 192 | |||||||
|
Bioconductor mailing list Resource Report Resource Website 1+ mentions |
Bioconductor mailing list (RRID:SCR_012915) | Bioconductor mailing list | data or information resource, feed, narrative resource, listserv | This mailing list is for announcements about Bioconductor and the availability of new code and questions and answers about problems and solutions using Bioconductor. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_01705 | SCR_012915 | 2026-08-05 10:45:54 | 2 | ||||||||||
|
NCBI Assembly Archive Viewer Resource Report Resource Website 100+ mentions |
NCBI Assembly Archive Viewer (RRID:SCR_012917) | NCBI Assembly Archive Viewer | data or information resource, data repository, data set, storage service resource, service resource | Database providing information on structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data. The Archive links the raw sequence information found in the Trace Archive with assembly information found in publicly available sequence repositories (GenBank/EMBL/DDBJ). | sequence alignment, sequence chromatogram, assembly, virus |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is related to: GenBank is related to: Trace Archive is related to: DNA DataBank of Japan (DDBJ) is related to: European Nucleotide Archive (ENA) |
OMICS_00890, r3d100012688 | http://www.ncbi.nlm.nih.gov/assembly, https://doi.org/10.17616/R31NJMA8 | http://www.ncbi.nlm.nih.gov/Traces/assembly/assmbrowser.cgi | SCR_012917 | Assembly Archive Viewer, NCBI Assembly, Assembly | 2026-08-05 10:45:50 | 274 | ||||||
|
GRASSIUS Resource Report Resource Website 10+ mentions |
GRASSIUS (RRID:SCR_012999) | GRASSIUS | data or information resource, data repository, data analysis service, database, storage service resource, production service resource, service resource, analysis service resource | A public resource composed of a collection of databases, computational and experimental resources that relate to the control of gene expression in the grasses, and their relationship with agronomic traits. As knowledge on the interactions of transcription factors (TFs) and cis-regulatory elements in the promoters of the genes that they regulate continues to accumulate, the information is acquired by GRASSIUS, either through contributions by the community, or by literature analysis. The overarching objective of GRASSIUS is to provide a one-stop resource that will facilitate research and communication within the plant community with regards to genome-wide regulation of gene expression processes. | transcription factor, coregulator, promoter sequence, transcription factor orf clone, blast, genome browser |
is listed by: OMICtools has parent organization: Ohio State University; Ohio; USA |
NSF | PMID:18987217 | Free | OMICS_00555 | SCR_012999 | Grass Regulatory Information Server | 2026-08-05 10:45:55 | 30 | |||||
|
NGSmethDB Resource Report Resource Website 1+ mentions |
NGSmethDB (RRID:SCR_012847) | NGSmethDB | data or information resource, data repository, database, storage service resource, service resource | A dedicated database for the storage, browsing and data mining of whole-genome, single-base-pair resolution methylomes. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20965971 | OMICS_01844, biotools:ngsmethdb | https://bio.tools/ngsmethdb | SCR_012847 | NGSmethDB - A database for NGS single-cytosine-resolution DNA methylation data | 2026-08-05 10:45:53 | 9 | ||||||
|
GenomeView Resource Report Resource Website 10+ mentions |
GenomeView (RRID:SCR_012968) | GenomeView | software resource, data or information resource, database | A next-generation stand-alone genome browser and editor initiated in the BSB group at VIB and currently developed at Broad Institute. | is listed by: OMICtools | PMID:22102585 | OMICS_00913 | SCR_012968 | 2026-08-05 10:45:51 | 36 | |||||||||
|
TopHat Resource Report Resource Website 5000+ mentions Rating or validation data |
TopHat (RRID:SCR_013035) | data processing software, software application, image analysis software, alignment software, data analysis software, sequence analysis software, software resource | Software tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions. | align, RNA-Seq, read, cDNA, sequencing, transcriptomics, fast, splice, junction, mapper, exon, analysis, bio.tools |
uses: Bowtie is used by: CIRCexplorer is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: HISAT2 has parent organization: University of Maryland; Maryland; USA has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Johns Hopkins University; Maryland; USA has parent organization: University of Washington; Seattle; USA works with: GeneScissors |
NHGRI R01 HG006102; NHGRI R01 HG006677 |
PMID:23618408 PMID:19289445 DOI:10.1093/bioinformatics/btp120 |
Free, Available for download, Freely available | biotools:tophat, OMICS_01257 | https://github.com/infphilo/tophat, https://bio.tools/tophat, https://sources.debian.org/src/tophat/ | http://tophat.cbcb.umd.edu/ | SCR_013035 | tophat, TopHat1, Tophat2 | 2026-08-05 10:45:55 | 9575 | ||||
|
MitoBreak Resource Report Resource Website 10+ mentions |
MitoBreak (RRID:SCR_012949) | MitoBreak | data or information resource, data repository, database, storage service resource, service resource | Database with curated datasets of mitochondrial DNA (mtDNA) rearrangements. Users may submit new mtDNA rearrangements. | mitochondrial dna rearrangement, mitochondrial dna, deletion, duplication, linear, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24170808 | Free, The community can contribute to this resource | biotools:mitobreak, OMICS_01640 | https://bio.tools/mitobreak | SCR_012949 | 2026-08-05 10:45:54 | 10 | ||||||
|
minfi Resource Report Resource Website 100+ mentions |
minfi (RRID:SCR_012830) | minfi | data processing software, software application, data visualization software, data analysis software, software resource | Software tools for analyzing and visualizing Illumina''s 450k array data. | Illumina, array data, Analyze Illumina Infinium DNA methylation arrays, DNA methylation array, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: SWAN has parent organization: Bioconductor |
PMID:28035024 | Free, Available for download, Freely available | biotools:minfi, OMICS_00799, BioTools:minfi | https://bio.tools/minfi, https://bio.tools/minfi, https://bio.tools/minfi | SCR_012830 | 2026-08-05 10:45:53 | 390 | ||||||
|
affy Resource Report Resource Website 1000+ mentions |
affy (RRID:SCR_012835) | Affy | software resource, data processing software, software application, data analysis software | Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis. | analysis, oligonucleotide, array, Affymetrix, process, probe, data, function, bio.tools |
is listed by: OMICtools is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: affydata is related to: R Project for Statistical Computing is related to: OMICtools |
Danish Biotechnology Instrument Center | PMID:14960456 | Free, Available for download, Freely available | BioTools:affy, OMICS_00740, biotools:affy | https://bio.tools/affy, https://sources.debian.org/src/r-bioc-affy/ | SCR_012835 | Affymetrix, analysis of Affymetrix GeneChip data at the probe level, analysis of Affymetrix GeneChip data | 2026-08-05 10:45:53 | 2996 | ||||
|
edgeR Resource Report Resource Website 10000+ mentions |
edgeR (RRID:SCR_012802) | edgeR | software resource, data processing software, software application, data analysis software | Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication. | empirical, analysis, digital, gene, expression, data, R, RNA-seq data, bio.tools |
is used by: Glimma is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: SARTools is related to: Bioconductor works with: tximport |
NHMRC 406657; Independent Research Institutes Infrastructure Support Scheme 361646; Victorian State Government OIS grant ; Melbourne International Research Scholarship ; Harris and IBS Honours scholarships |
PMID:19910308 DOI:10.1093/bioinformatics/btp616 |
Free, Available for download, Freely available | OMICS_01308, biotools:edger | https://bio.tools/edger, https://sources.debian.org/src/r-bioc-edger/ | SCR_012802 | edgeR, empirical analysis of digital gene expression data in R, Empirical analysis of Digital Gene Expression data in R | 2026-08-05 10:45:53 | 21899 | ||||
|
KEGG Resource Report Resource Website 10000+ mentions |
KEGG (RRID:SCR_012773) | KEGG | data or information resource, portal, web service, data access protocol, topical portal, database, software resource, data analysis service, production service resource, service resource, analysis service resource | Integrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information. In particular, gene catalogs in completely sequenced genomes are linked to higher-level systemic functions of cell, organism, and ecosystem. Analysis tools are also available. KEGG may be used as reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies. | model, pathway, functional hierarchy, module, cancer, disease, drug, drug classification, orthology, ortholog, genome, gene, protein, compound, classification, biochemical reaction, pathway, ligand, biosynthesis, pathway prediction, sequence, chemical structure, human, enzyme, database, molecular interaction, metabolism, metabolomics, cellular process, structure, drug development, reaction, cell |
is used by: NIF Data Federation is used by: Arabidopsis Reactome is used by: LIPID MAPS Proteome Database is used by: globaltest is used by: MitoMiner is used by: Database for Annotation Visualization and Integrated Discovery is used by: Biochemical Pathways Reaction Kinetics Database is used by: Ultimate Rough Aggregation of Metabolic Map is used by: GEMINI is used by: In vivo - In silico Metabolite Database is listed by: 3DVC is listed by: OMICtools is affiliated with: Kyoto Encyclopedia of Genes and Genomes Expression Database is related to: PathCase Pathways Database System is related to: ExplorEnz is related to: NCBI BioSystems Database is related to: Allen Institute Neurowiki is related to: eQuilibrator is related to: GeneTrail is related to: KegTools is related to: PRODORIC is related to: hiPathDB - human integrated Pathway DB with facile visualization is related to: METLIN is related to: Kidney and Urinary Pathway Knowledge Base is related to: DAVID is related to: ConsensusPathDB is related to: ENZYME is related to: FlyMine is related to: Babelomics is related to: SynSysNet is related to: Cotton EST Database is related to: Integrated Molecular Interaction Database is related to: SEGS is related to: INMEX is related to: BioExtract is related to: ClueGO is related to: MalaCards is related to: TrED is related to: FunTree is related to: MOPED - Model Organism Protein Expression Database is related to: ProOpDB is related to: KOBAS is related to: GeneTerm Linker is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit is related to: GeneCodis is related to: FunNet - Transcriptional Networks Analysis is related to: LegumeIP is related to: Algal Functional Annotation Tool is related to: aGEM is related to: DINIES is related to: KEGG PATHWAY Database is related to: ShinyGO is related to: KEGGREST has parent organization: Kyoto University; Kyoto; Japan has parent organization: University of Tokyo; Tokyo; Japan is parent organization of: KegTools works with: DIANA-mirPath works with: MiMeDB |
Japanese Ministry of Education Culture Sports Science and Technology MEXT ; Japan Science and Technology Agency |
PMID:22700311 PMID:22130871 PMID:22080510 PMID:19880382 PMID:19172790 PMID:18428742 PMID:18287706 PMID:18077471 PMID:16381885 PMID:16014746 PMID:14681412 PMID:12539951 PMID:11752249 PMID:10928937 PMID:10592173 PMID:9847135 |
Restricted | nlx_31015, OMICS_01583, OMICS_03010, OMICS_01582, OMICS_03974, OMICS_05434, OMICS_05360 | http://www.genome.jp/kegg/ | SCR_012773 | KEGG - Kyoto Encyclopedia of Genes and Genomes, Kyoto Encyclopedia of Genes and Genomes | 2026-08-05 10:45:52 | 75877 |
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