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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
REDItools Resource Report Resource Website 100+ mentions |
REDItools (RRID:SCR_012133) | software resource | A suite of python scripts to perform high-throughput investigation of RNA editing using next-generation sequencing data. | standalone software, illumina, roche, pacific biosciences, life technologies, python, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code |
PMID:23742983 | MIT License | biotools:reditools, OMICS_05860 | https://bio.tools/reditools | SCR_012133 | 2026-08-29 11:24:16 | 152 | |||||||
|
PrimerProspector Resource Report Resource Website 10+ mentions |
PrimerProspector (RRID:SCR_012136) | software resource | A pipeline of software programs to design and analyze PCR primers. It is built in Python using the open-source PyCogent toolkit. | standalone software, python |
is listed by: OMICtools has parent organization: SourceForge |
PMID:21349862 | OMICS_05884 | SCR_012136 | 2026-08-29 11:24:16 | 26 | |||||||||
|
iceLogo Resource Report Resource Website 100+ mentions |
iceLogo (RRID:SCR_012137) | software resource | Software that builds on probability theory to visualize significant conserved sequence patterns in multiple peptide sequence alignments against background (reference) sequence sets that can be tailored to the studied system and the used protocol. | standalone software, web app, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:19876014 | Apache License | biotools:icelogo, OMICS_05885 | https://bio.tools/icelogo | SCR_012137 | 2026-08-29 11:24:13 | 185 | |||||||
|
Musite Resource Report Resource Website 10+ mentions |
Musite (RRID:SCR_012141) | software resource | A Java-based standalone application for predicting both general and kinase-specific protein phosphorylation sites. | standalone software, java |
is listed by: OMICtools has parent organization: SourceForge |
PMID:20702892 | OMICS_05941 | SCR_012141 | 2026-08-29 11:24:20 | 13 | |||||||||
|
AMS Resource Report Resource Website |
AMS (RRID:SCR_012140) | software resource | Software that predicts the wide selection of 88 different types of the single amino acid post-translational modifications (PTM) in protein sequences. The source code and precompiled binaries of brainstorming tool are available under Apache licensing. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:22555647 | Apache License | OMICS_05934, biotools:ams | https://bio.tools/ams | SCR_012140 | AutoMotif Service | 2026-08-29 11:24:13 | 0 | ||||||
|
PhosphoSiteAnalyzer Resource Report Resource Website |
PhosphoSiteAnalyzer (RRID:SCR_012142) | software resource | A bioinformatical software tool for analyzing (quantitative) phosphoproteome datasets. The program retrieves kinase-substrate predictions from NetworKIN and contains various statistical modules for futher analysis. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:22471441 | Free, Public | biotools:phosphositeanalyzer, OMICS_05951 | https://bio.tools/phosphositeanalyzer | SCR_012142 | 2026-08-29 11:24:16 | 0 | |||||||
|
HLAforest Resource Report Resource Website 1+ mentions |
HLAforest (RRID:SCR_012146) | software resource | Software that predicts HLA haplotype by hierarchically weighting reads and using an iterative, greedy, top down pruning technique. HLAforest uses BioPerl to read in FASTA files. Alignments use Bow tie, although any alignment tool can be used to generate SAM alignments for use as input to HLAforest. | standalone software, perl |
is listed by: OMICtools has parent organization: Google Code |
PMID:23840783 | Free for academic use, Apache License | OMICS_06170 | SCR_012146 | 2026-08-29 11:24:16 | 6 | ||||||||
|
DNAcopy Resource Report Resource Website 100+ mentions |
DNAcopy (RRID:SCR_012560) | DNAcopy | software resource | Software that segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
OMICS_00720, biotools:dnacopy | https://bio.tools/dnacopy, https://sources.debian.org/src/r-bioc-dnacopy/ | SCR_012560 | 2026-08-29 11:24:20 | 349 | ||||||||
|
ExiMiR Resource Report Resource Website 1+ mentions |
ExiMiR (RRID:SCR_012753) | ExiMiR | software resource | R functions for the normalization of Exiqon miRNA array data. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00783 | SCR_012753 | 2026-08-29 11:24:22 | 1 | ||||||||||
|
CNV Workshop Resource Report Resource Website 1+ mentions |
CNV Workshop (RRID:SCR_012635) | CNV Workshop | software resource | Software for a web-enabled platform for analyzing genome variation such as copy number variation (CNV). |
is listed by: OMICtools has parent organization: SourceForge |
GNU Affero General Public License | OMICS_00715 | SCR_012635 | 2026-08-29 11:24:19 | 1 | |||||||||
|
motifRG Resource Report Resource Website 1+ mentions |
motifRG (RRID:SCR_012602) | motifRG | software resource | Software tools for discriminative motif discovery using regression methods. |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24162561 | Free | OMICS_00487 | SCR_012602 | motifRG - A package for discriminative motif discovery designed for high throughput sequencing dataset | 2026-08-29 11:24:20 | 5 | |||||||
|
MiRaGE Resource Report Resource Website 10+ mentions |
MiRaGE (RRID:SCR_012738) | MiRaGE | software resource | Software package that contains functions for inference of target gene regulation by miRNA, based on only target gene expression profile. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00785 | SCR_012738 | 2026-08-29 11:24:21 | 33 | ||||||||||
|
CexoR Resource Report Resource Website |
CexoR (RRID:SCR_012769) | CexoR | software resource | Software for strand specific peak-pair calling in ChIP-exo replicates. |
is listed by: OMICtools has parent organization: Bioconductor |
MIT License | OMICS_00519 | SCR_012769 | CexoR: An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates | 2026-08-29 11:24:32 | 0 | ||||||||
|
edgeR Resource Report Resource Website 10000+ mentions |
edgeR (RRID:SCR_012802) | edgeR | data analysis software, data processing software, software application, software resource | 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 |
Harris and IBS Honours scholarships ; Independent Research Institutes Infrastructure Support Scheme 361646; Melbourne International Research Scholarship ; NHMRC 406657; Victorian State Government OIS grant |
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 | 2026-08-29 11:24:34 | 23868 | ||||
|
MotifLab Resource Report Resource Website 1+ mentions |
MotifLab (RRID:SCR_012649) | MotifLab | software resource | Software for a general workbench for analyzing regulatory sequence regions and discovering transcription factor binding sites and cis-regulatory modules. |
is listed by: OMICtools has parent organization: Norwegian University of Science and Technology; Trondheim; Norway |
Research Council of Norway | PMID:23323883 | Acknowledgement requested, Free, Public | OMICS_00486 | SCR_012649 | 2026-08-29 11:24:30 | 2 | |||||||
|
KEGG Resource Report Resource Website 10000+ mentions |
KEGG (RRID:SCR_012773) | KEGG | analysis service resource, data access protocol, data analysis service, data or information resource, database, portal, production service resource, service resource, software resource, topical portal, web service | 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 |
Japan Science and Technology Agency ; Japanese Ministry of Education Culture Sports Science and Technology MEXT |
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 | 2026-08-29 11:24:32 | 81488 | ||||
|
tRanslatome Resource Report Resource Website 1+ mentions |
tRanslatome (RRID:SCR_012810) | tRanslatome | software resource | Detection of differentially expressed genes (DEGs) from the comparison of two biological conditions among different levels of gene expression, using several statistical methods: Rank Product, t-test, SAM, Limma, ANOTA, DESeq, edgeR. |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24222209 | Free | OMICS_01316 | SCR_012810 | tRanslatome - Comparison between multiple levels of gene expression | 2026-08-29 11:24:34 | 2 | |||||||
|
BEDOPS Resource Report Resource Website 100+ mentions |
BEDOPS (RRID:SCR_012865) | BEDOPS | software resource | A suite of tools to address common questions raised in genomic studies - mostly with regard to overlap and proximity relationships between data sets. |
is listed by: OMICtools is listed by: Debian |
PMID:22576172 DOI:10.1093/bioinformatics/bts277 |
GNU General Public License, v3 | OMICS_00949 | https://sources.debian.org/src/bedops/ | SCR_012865 | BEDOPS: high-performance genomic feature operations | 2026-08-29 11:24:34 | 237 | ||||||
|
Bioconductor mailing list Resource Report Resource Website 1+ mentions |
Bioconductor mailing list (RRID:SCR_012915) | Bioconductor mailing list | data or information resource, feed, listserv, narrative resource | 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 | 2026-08-29 11:24:24 | 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, service resource, storage 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 | 2026-08-29 11:24:24 | 313 |
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