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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 | 2026-09-03 04:51:27 | 152 | |||||||
|
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 | 2026-09-03 04:51:42 | 185 | |||||||
|
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 | 2026-09-03 04:51:41 | 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 | 2026-09-03 04:51:48 | 0 | |||||||
|
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 | 2026-09-03 04:51:49 | 349 | ||||||||
|
AutoDock Resource Report Resource Website 10000+ mentions |
AutoDock (RRID:SCR_012746) | autodock | software resource | Software suite of automated docking tools. Designed to predict how small molecules, such as substrates or drug candidates, bind to receptor of known 3D structure. AutoDock consist of AutoDock 4 and AutoDock Vina. AutoDock 4 consists of autodock to perform docking of ligand to set of grids describing target protein, and autogrid to pre calculate these grids. | Small molecules receptor binding, automated docking tools, 3D structure, AutoDock 4, AutoDock Vina, ligand, docking |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Autogrid |
PMID:19399780 | Free, Available for download, Freely available | OMICS_01594, biotools:autodock | https://bio.tools/autodock, https://sources.debian.org/src/autodock/ | SCR_012746 | 2026-09-03 04:51:38 | 13612 | ||||||
|
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 | 2026-09-03 04:51:54 | 23868 | ||||
|
IMGT - the international ImMunoGeneTics information system Resource Report Resource Website 500+ mentions |
IMGT - the international ImMunoGeneTics information system (RRID:SCR_012780) | IMGT | analysis service resource, data analysis service, data or information resource, database, portal, production service resource, service resource, topical portal | A high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrate species, and in the immunoglobulin superfamily (IgSF), MHC superfamily (MhcSF) and related proteins of the immune system (RPI) of vertebrates and invertebrates, serving as the global reference in immunogenetics and immunoinformatics. IMGT provides a common access to sequence, genome and structure Immunogenetics data, based on the concepts of IMGT-ONTOLOGY and on the IMGT Scientific chart rules. IMGT works in close collaboration with EBI (Europe), DDBJ (Japan) and NCBI (USA). IMGT consists of sequence databases, genome database, structure database, and monoclonal antibodies database, Web resources and interactive tools. | immunogenetics, immunoinformatics, immunoglobulin, antibody, t cell receptor, major histocompatibility complex, immunoglobulin superfamily, major histocompatibility complex superfamily, protein, immune system, sequence, genome, structure, monoclonal antibody, gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: IMGT Repertoire has parent organization: Montpellier 2 University; Montpellier; France is parent organization of: IMGT/LIGM-DB is parent organization of: IMGT/GENE-DB is parent organization of: IMGT-ONTOLOGY is parent organization of: IMGT/V-QUEST is parent organization of: IMGT/HLA |
CNRS ; MESR ; Reseau National des Genopoles ; Region Languedoc-Roussillon ; European Union BIOMED1 BIOCT930038; European Union Biotechnology BIOTECH2 BIO4CT960037; European Union 5th PCRDT Quality of Life and Management of Living Resources QLG2-2000-01287; Agence Nationale de la recherche ANR BIOSYS06_135457; EU ImmunoGrid IST-028069 |
PMID:18978023 | nif-0000-03011, biotools:imgt | https://bio.tools/imgt | http://imgt.cines.fr | SCR_012780 | ImMunoGeneTics Information System, IMGT/LIGM, ImMunoGeneTics | 2026-09-03 04:51:58 | 779 | ||||
|
Krona Resource Report Resource Website 50+ mentions |
Krona (RRID:SCR_012785) | Krona | software resource | Software that allows hierarchical data to be explored with zoomable pie charts. | bio.tools |
is listed by: bio.tools has parent organization: SourceForge |
PMID:21961884 | OMICS_01498, biotools:krona | https://bio.tools/krona | SCR_012785 | Krona - Hierarchical data browser | 2026-09-03 04:51:54 | 97 | ||||||
|
SALT Resource Report Resource Website 1000+ mentions |
SALT (RRID:SCR_003187) | SALT | software resource | Software that can accurately and sensitivity classify short reads of next-generation sequencing (NGS) into protein domain families. It is based on profile HMM and a supervised graph contribution algorithm. Compared to existing tools, it has high sensitivity and specificity in classifying short reads into their native domain families. | next-generation sequencing, protein, protein domain, short read, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23782615 | Free, Available for download, Freely available | OMICS_01565, biotools:salt | https://bio.tools/salt | SCR_003187 | SALT - Protein domain classifier | 2026-09-03 04:46:08 | 1307 | |||||
|
PredictNLS Resource Report Resource Website 10+ mentions |
PredictNLS (RRID:SCR_003133) | PredictNLS | analysis service resource, data analysis service, production service resource, service resource, software resource | Software automated tool for analysis and determination of Nuclear Localization Signals (NLS). Predicts that your protein is nuclear or finds out whether your potential NLS is found in our database. The program also compiles statistics on the number of nuclear/non-nuclear proteins in which your potential NLS is found. Finally, proteins with similar NLS motifs are reported, and the experimental paper describing the particular NLS are given. | bio.tools, nuclear localization signal, protein, protein sequence |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: ROSTLAB has parent organization: Columbia University; New York; USA |
DOI:10.1093/embo-reports/kvd092 | Free, Available for download, Freely available | nif-0000-31416, OMICS_01633, SCR_008553, biotools:predictnls | https://www.rdocumentation.org/packages/propagate/versions/1.0-4/topics/predictNLS | SCR_003133 | Prediction and Analysis of Nuclear Localization Signals | 2026-09-03 04:46:06 | 33 | |||||
|
NovelSeq Resource Report Resource Website |
NovelSeq (RRID:SCR_003136) | NovelSeq | software resource | Software pipeline to detect novel sequence insertions using high throughput paired-end whole genome sequencing data. | sequence, insertion, genome sequencing, genome, next-generation sequencing, illumina, unix, linux, c, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SPLITREAD has parent organization: Simon Fraser University; British Columbia; Canada has parent organization: SourceForge |
PMID:20385726 | Free, Available for download, Freely available | biotools:novelseq, nlx_156791, OMICS_02164 | https://mybiosoftware.com/novelseq-1-0-2-sequence-insertions-detection.html#google_vignette | SCR_003136 | NovelSeq: Novel Sequence Insertion Detection | 2026-09-03 04:46:03 | 0 | |||||
|
mrCaNaVaR Resource Report Resource Website 10+ mentions |
mrCaNaVaR (RRID:SCR_003135) | mrCaNaVaR | software resource | Copy number caller that analyzes the whole-genome next-generation sequence mapping read depth to discover large segmental duplications and deletions. It also has the capability of predicting absolute copy numbers of genomic intervals. | genome, next-generation sequence, duplication, deletion, copy number variant, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SPLITREAD has parent organization: SourceForge |
Free, Freely available | OMICS_02138, nlx_156790, biotools:mrcanavar | https://bio.tools/mrcanavar | SCR_003135 | mrCaNaVaR - micro-read Copy Number Variant Regions, micro-read Copy Number Variant Regions | 2026-09-03 04:45:57 | 16 | ||||||
|
SplicingCompass Resource Report Resource Website 1+ mentions |
SplicingCompass (RRID:SCR_003249) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for detection of differential splicing between two different conditions using RNA-Seq data. | differential splicing, splicing event, exon removal, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23449093 | Free, Available for download, Freely available | biotools:splicingcompass, OMICS_01340 | https://github.com/KoenigLabNM/SplicingCompass | SCR_003249 | Splicing Compass | 2026-09-03 04:46:18 | 2 | ||||||
|
MultiLoc Resource Report Resource Website 10+ mentions |
MultiLoc (RRID:SCR_003151) | MultiLoc | analysis service resource, data analysis service, production service resource, service resource, software resource | An extensive high-performance subcellular protein localization prediction system that incorporates phylogenetic profiles and Gene Ontology terms to yield higher accuracies compared to its previous version. Moreover, it outperforms other prediction systems in two benchmarks studies. A downloadable version of MultiLoc2 for local use is also available. | subcellular localization, protein, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tubingen; Tubingen; Germany |
PMID:19723330 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01628, biotools:multiloc2 | https://bio.tools/multiloc2 | SCR_003151 | 2026-09-03 04:46:04 | 41 | ||||||
|
Primer3 Resource Report Resource Website 10000+ mentions |
Primer3 (RRID:SCR_003139) | Primer3 | analysis service resource, data analysis service, production service resource, service resource, software resource | Tool used to design PCR primers from DNA sequence - often in high-throughput genomics applications. It does everything from mispriming libraries to sequence quality data to the generation of internal oligos. | primer, primer design, polymerase chain reaction, pcr primer, dna sequence, c, perl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Primer3Plus is related to: Primer-BLAST has parent organization: University of Tartu; Tartu; Estonia |
NHGRI R01-HG00257; NHGRI P50-HG00098 |
PMID:22730293 PMID:17379693 DOI:10.1385/1-59259-192-2:365 DOI:10.1385/1-59259-192-2:365 |
Free, Freely available | nlx_156833, OMICS_02325, biotools:primer3 | http://bioinfo.ut.ee/primer3-0.4.0/, http://sourceforge.net/projects/primer3/, http://frodo.wi.mit.edu/primer3, https://bio.tools/primer3, https://sources.debian.org/src/primer3/, https://sources.debian.org/src/primer3/ | SCR_003139 | Primer3web - Pick primers from a DNA sequence, Primer3 - PCR primer design tool, Primer3web | 2026-09-03 04:46:12 | 11934 | ||||
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Mouse Phenome Database (MPD) Resource Report Resource Website 100+ mentions |
Mouse Phenome Database (MPD) (RRID:SCR_003212) | MPD | data or information resource, data repository, database, experimental protocol, narrative resource, service resource, storage service resource | Database enables integration of genomic and phenomic data by providing access to primary experimental data, data collection protocols and analysis tools. Data represent behavioral, morphological and physiological disease-related characteristics in naive mice and those exposed to drugs, environmental agents or other treatments. Collaborative standardized collection of measured data on laboratory mouse strains to characterize them in order to facilitate translational discoveries and to assist in selection of strains for experimental studies. Includes baseline phenotype data sets as well as studies of drug, diet, disease and aging effect., protocols, projects and publications, and SNP, variation and gene expression studies. Provides tools for online analysis. Data sets are voluntarily contributed by researchers from variety of institutions and settings, or retrieved by MPD staff from open public sources. MPD has three major types of strain-centric data sets: phenotype strain surveys, SNP and variation data, and gene expression strain surveys. MPD collects data on classical inbred strains as well as any fixed-genotype strains and derivatives that are openly acquirable by the research community. New panels include Collaborative Cross (CC) lines and Diversity Outbred (DO) populations. Phenotype data include measurements of behavior, hematology, bone mineral density, cholesterol levels, endocrine function, aging processes, addiction, neurosensory functions, and other biomedically relevant areas. Genotype data are primarily in the form of single-nucleotide polymorphisms (SNPs). MPD curates data into a common framework by standardizing mouse strain nomenclature, standardizing units (SI where feasible), evaluating data (completeness, statistical power, quality), categorizing phenotype data and linking to ontologies, conforming to internal style guides for titles, tags, and descriptions, and creating comprehensive protocol documentation including environmental parameters of the test animals. These elements are critical for experimental reproducibility. | female, genomic location, genotype, inbred strain, male, mouse strain, phenome, phenotype, qtl, reference data, single-nucleotide polymorphism, strain allele, strain characteristic, strain, trait, gene expression, variation, hypothesis testing, data set, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: Integrated Datasets is used by: NIH Heal Project is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Special Mouse Strains Resource is related to: Vertebrate Trait Ontology is related to: GenomeMUSter has parent organization: Jackson Laboratory |
NHGRI HG003057; NHLBI HL66611; NIA AG025707; NIA AG038070; NIDA ; NIDA DA028420; NIMH MH071984 |
PMID:24243846 PMID:22102583 PMID:18987003 PMID:17151079 |
Free, Freely available | biotools:mpd, nif-0000-03160, r3d100010101 | https://bio.tools/mpd, https://doi.org/10.17616/R3PC7F | http://www.jax.org/phenome | SCR_003212 | Mouse Phenome Database | 2026-09-03 04:46:01 | 230 | |||
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Pipeliner Resource Report Resource Website 1+ mentions |
Pipeliner (RRID:SCR_003171) | software resource | Software for evaluating the performance of bioinformatics pipelines for Next Generation re-Sequencing. | standalone software, c++, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24890372 | Free, Available for download, Freely available | OMICS_04844, biotools:pipeliner | https://bio.tools/pipeliner | SCR_003171 | 2026-09-03 04:46:02 | 7 | |||||||
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Database of Interacting Proteins (DIP) Resource Report Resource Website 100+ mentions |
Database of Interacting Proteins (DIP) (RRID:SCR_003167) | DIP | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | Database to catalog experimentally determined interactions between proteins combining information from a variety of sources to create a single, consistent set of protein-protein interactions that can be downloaded in a variety of formats. The data were curated, both, manually and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. Because the reliability of experimental evidence varies widely, methods of quality assessment have been developed and utilized to identify the most reliable subset of the interactions. This CORE set can be used as a reference when evaluating the reliability of high-throughput protein-protein interaction data sets, for development of prediction methods, as well as in the studies of the properties of protein interaction networks. Tools are available to analyze, visualize and integrate user's own experimental data with the information about protein-protein interactions available in the DIP database. The DIP database lists protein pairs that are known to interact with each other. By interact they mean that two amino acid chains were experimentally identified to bind to each other. The database lists such pairs to aid those studying a particular protein-protein interaction but also those investigating entire regulatory and signaling pathways as well as those studying the organization and complexity of the protein interaction network at the cellular level. Registration is required to gain access to most of the DIP features. Registration is free to the members of the academic community. Trial accounts for the commercial users are also available. | blast, cellular network, ligand-receptor complex, ligand, network, protein, protein interaction, protein ligand, protein-protein interaction, protein receptor, receptor, sequence, interaction, regulatory pathway, signaling pathway, protein binding, bio.tools, FASEB list |
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: OMICtools is listed by: re3data.org is listed by: NIH Data Sharing Repositories is listed by: bio.tools is listed by: Debian is related to: IMEx - The International Molecular Exchange Consortium is related to: IMEx - The International Molecular Exchange Consortium is related to: MPIDB is related to: TissueNet - The Database of Human Tissue Protein-Protein Interactions is related to: InteroPorc is related to: Interaction Reference Index is related to: ConsensusPathDB is related to: NIH Data Sharing Repositories is related to: PSICQUIC Registry is related to: Agile Protein Interactomes DataServer has parent organization: University of California at Los Angeles; California; USA |
NIGMS | PMID:14681454 | Free, Available for download, Freely available | OMICS_01905, nif-0000-00569, r3d100010882, biotools:dip | https://dip.doe-mbi.ucla.edu/dip/Main.cgi, https://bio.tools/dip, https://doi.org/10.17616/R3431F | SCR_003167 | , Database of Interacting Proteins, DIP, Database of Interacting Proteins (DIP) | 2026-09-03 04:45:58 | 167 | ||||
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Piano Resource Report Resource Website 100+ mentions |
Piano (RRID:SCR_003200) | data analysis software, data processing software, software application, software resource | Software R-package for running gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. The Piano package contains functions for combining the results of multiple runs of gene set analyses. | r, omics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Chalmers University of Technology; Gothenburg; Sweden has parent organization: Bioconductor |
PMID:23444143 | Free, Available for download, Freely available | OMICS_01558, biotools:piano | https://bio.tools/piano | SCR_003200 | 2026-09-03 04:46:07 | 188 |
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