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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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IMEx - The International Molecular Exchange Consortium Resource Report Resource Website 100+ mentions |
IMEx - The International Molecular Exchange Consortium (RRID:SCR_002805) | IMEx | community building portal, organization portal, storage service resource, data or information resource, consortium, database, service resource, portal, data repository | Interaction database from international collaboration between major public interaction data providers who share curation effort and develop set of curation rules when capturing data from both directly deposited interaction data or from publications in peer reviewed journals. Performs complete curation of all protein-protein interactions experimentally demonstrated within publication and makes them available in single search interface on common website. Provides data in standards compliant download formats. IMEx partners produce their own separate resources, which range from all encompassing molecular interaction databases, such as are maintained by IntAct, MINT and DIP, organism-centric resources such as BioGrid or MPIDB or biological domain centric, such as MatrixDB. They have committed to making records available, via PSICQUIC webservice, which have been curated to IMEx rules and are available to users as single, non-redundant set of curated publications which can be searched at the IMEx website. Data is made available in standards-compliant tab-deliminated and XML formats, enabling to visualize data using wide range of tools. Consortium is open to participation of additional partners and encourages deposition of data, prior to publication, and will supply unique accession numbers which may be referenced within final article. Submitters may send their data directly to any of member databases using variety of formats, but should conform to guidelines as to minimum information required to describe data. | protein-protein interaction, nonredundant, protein interaction, interaction, proteomics, metadata standard, short course, molecular interaction, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is affiliated with: MINT is related to: MatrixDB is related to: MPIDB is related to: Database of Interacting Proteins (DIP) is related to: Database of Interacting Proteins (DIP) is related to: InnateDB is related to: IntAct is related to: Interaction Reference Index is related to: MPIDB is related to: UniProt is related to: InnateDB is related to: MatrixDB is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: I2D is related to: Molecular Connections NetPro is related to: SIB Swiss Institute of Bioinformatics is related to: IntAct is related to: PSI-MI is related to: PSICQUIC Registry is related to: mentha is related to: Bioconductor has parent organization: European Bioinformatics Institute works with: CellPhoneDB works with: Cytoscape works with: IntAct works with: MINT works with: MPact: Representation of Interaction Data at MIPS works with: Molecular Connections NetPro works with: Biological General Repository for Interaction Datasets (BioGRID) works with: InnateDB works with: BIND |
European Union | PMID:22453911 PMID:17893861 |
Free, Freely available, Available for download | nif-0000-00447, OMICS_01545, r3d100010669, biotools:imex | http://imex.sourceforge.net/ https://bio.tools/imex https://doi.org/10.17616/R3090W |
SCR_002805 | The International Molecular Exchange Consortium, International Molecular Exchange Consortium | 2026-02-17 09:59:59 | 144 | ||||
|
GreenPhylDB Resource Report Resource Website 10+ mentions |
GreenPhylDB (RRID:SCR_002834) | GreenPhylDB | data or information resource, production service resource, analysis service resource, database, service resource, data analysis service | A database designed for plant comparative and functional genomics based on complete genomes. It comprises complete proteome sequences from the major phylum of plant evolution. The clustering of these proteomes was performed to define a consistent and extensive set of homeomorphic plant families. Based on this, lists of gene families such as plant or species specific families and several tools are provided to facilitate comparative genomics within plant genomes. The analyses follow two main steps: gene family clustering and phylogenomic analysis of the generated families. Once a group of sequences (cluster) is validated, phylogenetic analyses are performed to predict homolog relationships such as orthologs and ultraparalogs. | comparative genomics, genome, functional genomics, genomics, gene family, homolog, bio.tools |
uses: Gene Ontology is listed by: bio.tools is listed by: Debian has parent organization: CIRAD |
PMID:20864446 | Free, Freely available, Available for download | biotools:greenphyldb, nif-0000-02928 | http://greenphyl.cirad.fr http://www.greenphyl.org/v3/ https://bio.tools/greenphyldb |
SCR_002834 | 2026-02-17 09:59:59 | 19 | ||||||
|
ANDES Resource Report Resource Website 10+ mentions |
ANDES (RRID:SCR_002791) | software application, data processing software, data analysis software, software resource, software toolkit | Software library and a suite of applications, written in Perl and R, for deep sequencing statistical analyses. | deep sequencing, biomarker detection, statistical analysis, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20633290 | Free, Freely available, Available for download | biotools:andes, OMICS_01119 | https://bio.tools/andes | SCR_002791 | Statistical tools for the Analyses of Deep Sequencing (ANDES), Statistical tools for the Analyses of Deep Sequencing, Statistical tools for the ANalyses of Deep Sequencing | 2026-02-17 10:00:03 | 25 | ||||||
|
NCBI database of Genotypes and Phenotypes (dbGap) Resource Report Resource Website 500+ mentions |
NCBI database of Genotypes and Phenotypes (dbGap) (RRID:SCR_002709) | dbGaP | storage service resource, data or information resource, database, service resource, data repository | Database developed to archive and distribute clinical data and results from studies that have investigated interaction of genotype and phenotype in humans. Database to archive and distribute results of studies including genome-wide association studies, medical sequencing, molecular diagnostic assays, and association between genotype and non-clinical traits. | clinical, trial, genotype, interaction, homology, cell, morphology, interaction, phenotype, molecular diagnosis, genetic recombination, gold standard, bio.tools |
is used by: International Genomics of Alzheimers Project is used by: NIDDK Inflammatory Bowel Disease Genetics Consortium is used by: NIH Heal Project is used by: Genomic Data Commons Data Portal (GDC Data Portal) is recommended by: National Library of Medicine 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 listed by: re3data.org is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian is related to: NIDDK Central Repository is related to: eMERGE Network: electronic Medical Records and Genomics is related to: Framingham Heart Study is related to: PhenoExplorer is related to: Chronic Renal Insufficiency Cohort Study is related to: DbGaP Cleaner is related to: Psychiatric Genomics Consortium is related to: ISCA Consortium is related to: Allen Institute for Brain Science has parent organization: NCBI is parent organization of: Resource for Genetic Epidemiology Research on Adult Health and Aging |
NLM | PMID:24297256 PMID:17898773 |
Restricted | nif-0000-23342, OMICS_00263, biotools:dbgap, r3d100010788 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=gap https://bio.tools/dbgap https://doi.org/10.17616/R3GS4K |
SCR_002709 | database of Genotypes and Phenotypes (dbGaP), dbGaP, NCBI, Database of Genotypes and Phenotypes | 2026-02-17 10:00:01 | 683 | ||||
|
discoSnp Resource Report Resource Website 1+ mentions |
discoSnp (RRID:SCR_002612) | software application, data processing software, data analysis software, software resource, sequence analysis software | Software designed for discovering Single Nucleotide Polymorphism (SNP) from raw sets of reads obtained with Next Generation Sequencers (NGS). | single nucleotide polymorphism, snp discovery, discover snp, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
SOFIPROTEOL under the FASO project PEAPOL ; INRIA ANR-12-BS02-0008 |
PMID:25404127 | Free, Freely available | biotools:discosnp, OMICS_00267 | https://bio.tools/discosnp https://sources.debian.org/src/discosnp/ |
SCR_002612 | DiscoSnp++, discovering Single Nucleotide Polymorphism, discovering Single Nucleotide Polymorphism (discoSNP) | 2026-02-17 09:59:49 | 9 | |||||
|
SuperPred: Drug classification and target prediction Resource Report Resource Website |
SuperPred: Drug classification and target prediction (RRID:SCR_002691) | SuperPred | data access protocol, data or information resource, database, web service, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 24,2025. Publicly available web-server to predict medical indication areas based on properties and similarity of chemical compounds. The web-server translates a user-defined molecule into a structural fingerprint that is compared to about 6300 drugs, which are enriched by 7300 links to molecular targets of the drugs, derived through text mining followed by manual curation. Links to the affected pathways are provided. The similarity to the medical compounds is expressed by the Tanimoto coefficient that gives the structural similarity of two compounds. A similarity score higher than 0.85 results in correct ATC prediction for 81% of all cases. As the biological effect is well predictable, if the structural similarity is sufficient, the web-server allows prognoses about the medical indication area of novel compounds and to find new leads for known targets. The combination of physicochemical property and similarity searching provides the possibility to detect new biologically active compounds and novel targets for drug-like compounds. SuperPred can be applied for drug repositioning purposes, too. A further intention of SuperPred is to find side effects elicited by drugs caused through off-target hits. | drug, drug class, drug target, addiction, anatomical therapeutic chemical, application area, biological activity, chemical, chemical classification, chemical property, classification, compound, molecular target, molecule, nervous system, pathway, pharmacological property, physicochemical property, prediction, activity spectra, substance, structural similarity, structure, tanimoto coefficient, tanimoto score, target prediction, target-prediction server, therapeutic approach, therapeutic property, drug classification, target prediction, similarity score, target, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany |
SFB 449 ; IRTG Berlin-Boston-Kyoto and Deutsche Krebshilfe. ; DFG |
PMID:18499712 PMID:24878925 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:superpred, nif-0000-00415 | https://bio.tools/superpred | SCR_002691 | 2026-02-17 10:00:02 | 0 | |||||
|
Rainbow Resource Report Resource Website 10+ mentions |
Rainbow (RRID:SCR_002724) | software application, data processing software, data analysis software, software resource, sequence analysis software | Software developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. | software, tool, clustering, assembling, short, read, restriction, site, DNA, sequence, analysis, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:22942077 DOI:10.1093/bioinformatics/bts482 |
Free, Freely available, Available for download | SCR_015992, OMICS_03722, biotools:rainbow | https://bio.tools/rainbow https://sources.debian.org/src/bio-rainbow/ |
SCR_002724 | RAD-seq: Restriction-site Associated DNA sequencing, Bio-rainbow, RAD-seq | 2026-02-17 10:00:02 | 41 | ||||||
|
Coding Potential Calculator Resource Report Resource Website 100+ mentions |
Coding Potential Calculator (RRID:SCR_002764) | CPC | production service resource, analysis service resource, service resource, software resource, data analysis service | A Support Vector Machine-based classifier to assesses the protein-coding potential of a transcript based on six biologically meaningful sequence features. CPC can discriminate coding from noncoding transcripts with high accuracy and speed. In addition to predicting the coding potential of the input transcripts, the CPC web server also graphically displays detailed sequence features and additional annotations of the transcript that may facilitate users' further investigation. The coding potential calculator tool reads FASTA data format as input. | fasta, transcript, protein coding, coding potential, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Peking University; Beijing; China |
PMID:17631615 | Free, Freely available | biotools:cpc, rid_000106 | https://bio.tools/cpc | SCR_002764 | 2026-02-17 09:59:58 | 198 | ||||||
|
Primer3Plus Resource Report Resource Website 1000+ mentions |
Primer3Plus (RRID:SCR_003081) | Primer3Plus | production service resource, analysis service resource, source code, service resource, software resource, data analysis service | A web interface to the Primer3 primer design program as an enhanced alternative for the CGI- scripts that come with Primer3. | primer, dna sequence, primer design, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Primer3 has parent organization: Wageningen University and Research Centre; Gelderland; Netherlands |
Howard Hughes Medical Institute ; NHGRI R01-HG00257; NHGRI P50-HG00098 |
PMID:17485472 | Free, Freely available | biotools:primer3plus, OMICS_02347 | https://bio.tools/primer3plus | SCR_003081 | Primer3Plus - pick primers from a DNA sequence | 2026-02-17 09:59:55 | 1673 | ||||
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DIALIGN Resource Report Resource Website 10+ mentions |
DIALIGN (RRID:SCR_003041) | DIALIGN | data access protocol, production service resource, analysis service resource, service resource, software resource, web service, data analysis service | Tool for multiple sequence alignment using various sources of external information that is particularly useful to detect local homologies in sequences with low overall similarity. While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences. No gap penalty is used. This approach can be used for both global and local alignment, but it is particularly successful in situations where sequences share only local homologies. Several versions of DIALIGN are available online at GOBICS, http://dialign.gobics.de/ | dna, protein, sequence alignment, sequence, alignment, fasta, genome, genomic sequence, homology, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Bielefeld University; North Rhine-Westphalia; Germany |
PMID:15215344 PMID:23620293 DOI:10.1186/1748-7188-3-6 |
Free, Available for download, Freely available | nif-0000-30417, OMICS_24606, OMICS_00973, biotools:dialign-tx | http://dialign.gobics.de/ https://bio.tools/dialign-tx |
https://sources.debian.org/src/dialign-tx/ | SCR_003041 | DIALIGN at GOBICS | 2026-02-17 09:59:55 | 43 | ||||
|
PredictNLS Resource Report Resource Website 10+ mentions |
PredictNLS (RRID:SCR_003133) | PredictNLS | production service resource, analysis service resource, service resource, software resource, data analysis service | 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 | 2026-02-17 10:00:12 | 30 | |||||
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SplicingCompass Resource Report Resource Website 1+ mentions |
SplicingCompass (RRID:SCR_003249) | software application, data processing software, data analysis software, software resource, sequence analysis software | 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 | 2026-02-17 10:00:07 | 2 | ||||||
|
deFuse Resource Report Resource Website 50+ mentions |
deFuse (RRID:SCR_003279) | software application, data processing software, data analysis software, sequence analysis software, software resource, software toolkit | Software package for gene fusion discovery using RNA-Seq data. It uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries. | rna sequencing, gene fusion, paired end alignment, split read, fusion boundary, bio.tools |
uses: SAMTOOLS uses: Bowtie uses: BLAT uses: GMAP uses: R Project for Statistical Computing is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
British Columbia Cancer Foundation ; Vancouver General Hospital Foundation ; Genome Canada ; Michael Smith Foundation for Health Research ; Canadian Breast Cancer Foundation ; Canadian Institutes of Health Research's Bioinformatics Training Program |
PMID:21625565 | Free, Available for download, Freely available | biotools:defuse, OMICS_01345 | https://sourceforge.net/projects/defuse/ http://compbio.bccrc.ca/software/defuse/ https://bio.tools/defuse |
http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page | SCR_003279 | 2026-02-17 10:00:15 | 95 | |||||
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MultiLoc Resource Report Resource Website 10+ mentions |
MultiLoc (RRID:SCR_003151) | MultiLoc | production service resource, analysis service resource, service resource, software resource, data analysis service | 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 | 2026-02-17 10:00:05 | 40 | ||||||
|
Primer3 Resource Report Resource Website 10000+ mentions |
Primer3 (RRID:SCR_003139) | Primer3 | production service resource, analysis service resource, service resource, software resource, data analysis service | 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 | 2026-02-17 10:00:10 | 10957 | ||||
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Mouse Phenome Database (MPD) Resource Report Resource Website 100+ mentions |
Mouse Phenome Database (MPD) (RRID:SCR_003212) | MPD | narrative resource, storage service resource, data or information resource, database, service resource, experimental protocol, data repository | 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 |
NIDA ; NHGRI HG003057; NHLBI HL66611; NIA AG025707; NIA AG038070; NIMH MH071984; NIDA DA028420 |
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 | 2026-02-17 10:00:13 | 221 | |||
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Database of Interacting Proteins (DIP) Resource Report Resource Website 100+ mentions |
Database of Interacting Proteins (DIP) (RRID:SCR_003167) | DIP | storage service resource, data or information resource, production service resource, analysis service resource, database, service resource, data analysis service, data repository | 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) | 2026-02-17 10:00:11 | 153 | ||||
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Piano Resource Report Resource Website 100+ mentions |
Piano (RRID:SCR_003200) | data analysis software, software application, data processing software, 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 | 2026-02-17 10:00:13 | 182 | |||||||
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Solas Resource Report Resource Website 1+ mentions |
Solas (RRID:SCR_003168) | software application, data processing software, data analysis software, source code, software resource, sequence analysis software | Software package for the statistical language R, devoted to the analysis of next generation short read data of RNA-seq transcripts. It provides predictions of alternative exons in a single condition/cell sample, predictions of differential alternative exons between two conditions/cell samples, and quantification of alternative splice forms in a single condition/cell sample. | r statistical package, rna seq, exon prediction, exon splicing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: R Project for Statistical Computing has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany |
Free, Available for download, Freely available | biotools:solas, OMICS_01339 | https://bio.tools/solas | SCR_003168 | 2026-02-17 10:00:12 | 8 | ||||||||
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GenePattern Resource Report Resource Website 1000+ mentions |
GenePattern (RRID:SCR_003201) | GenePattern | data analysis software, software application, data processing software, software resource | A powerful genomic analysis platform that provides access to hundreds of tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research. | gene expression, analysis, genomic, pattern, proteomics, silico, snp, workflow, analysis pipeline, flow cytometry, rna-seq, data processing, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite is affiliated with: GenePattern Notebook is related to: TIGRESS has parent organization: Broad Institute |
NCI ; NIGMS |
PMID:16642009 | Free, Freely available | biotools:genepattern, OMICS_01855, nif-0000-30654 | https://bio.tools/genepattern | SCR_003201 | 2026-02-17 09:59:57 | 1078 |
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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 2U24DK097771-09.
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