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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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pickgene Resource Report Resource Website |
pickgene (RRID:SCR_001331) | pickgene | data analysis software, software application, software resource, data processing software | Software for adaptive Gene Picking for Microarray Expression Data Analysis. | microarray, gene expression, differential expression, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02007, biotools:pickgene | https://bio.tools/pickgene | SCR_001331 | 2026-08-06 09:25:22 | 0 | |||||||
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VCFtools Resource Report Resource Website 1000+ mentions |
VCFtools (RRID:SCR_001235) | data management software, software application, software resource | Software package for working with VCF files. Used to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.Implements various utilities for processing Variant Call Format files, including validation, merging, comparing. Provides general Perl API. | perl, genetic variation, variant call format, software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:21653522 DOI:10.1093/bioinformatics/btr330 |
Free, Available for download, Freely available | OMICS_02105, biotools:vcftools, SCR_012092, OMICS_05112 | https://bio.tools/vcftools, https://sources.debian.org/src/vcftools/ | http://vcftools.sourceforge.net/ | SCR_001235 | Variant Call Format Tools | 2026-08-06 09:25:21 | 4095 | |||||
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ShortFuse Resource Report Resource Website 1+ mentions |
ShortFuse (RRID:SCR_001107) | sequence analysis software, software resource, data analysis software, data processing software, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A software package with tools for identifying fusion transcripts from RNA-Seq data. It is written in C++, and has dependencies on packages from Python 2. | fusion transcripts, rna, sequence data, python 2, c++, sequence analysis software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:21330288 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:shortfuse, OMICS_01355 | https://bio.tools/shortfuse | SCR_001107 | 2026-08-06 09:25:19 | 1 | |||||||
|
metahdep Resource Report Resource Website |
metahdep (RRID:SCR_001225) | metahdep | data analysis software, software application, software resource, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies. | differential expression, microarray, gene expression, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:19648140 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:metahdep, OMICS_02121 | https://bio.tools/metahdep | SCR_001225 | metahdep - Hierarchical Dependence in Meta-Analysis | 2026-08-06 09:25:21 | 0 | |||||
|
globaltest Resource Report Resource Website 10+ mentions |
globaltest (RRID:SCR_001256) | globaltest | sequence analysis software, software resource, data analysis software, data processing software, software application | A software package that tests groups of covariates (or features) for association with a response variable. The package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms. | differential expression, go, microarray, one channel, pathway, bio.tools |
uses: KEGG is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: Bioconductor |
PMID:34046931 | Free, Available for download, Freely available | biotools:globaltest, OMICS_02084 | https://bio.tools/globaltest | SCR_001256 | 2026-08-06 09:25:21 | 30 | ||||||
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DSRC Resource Report Resource Website 1+ mentions |
DSRC (RRID:SCR_001005) | DSRC | data management software, software application, software resource | An application designed for compression of data files containing reads from DNA sequencing in FASTQ format. Its main features include multithreaded compression of FASTQ output, python and C++ libraries, and support for lossy IDs compression. | fastq, dna sequence, compression, multithread, data management software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:21252073 | Free, Available as binary, Available as source code | biotools:dsrc, OMICS_00955 | https://bio.tools/dsrc | SCR_001005 | DNA Sequence Reads Compression, DNA Sequence Reads Compression (DSRC) | 2026-08-06 09:25:18 | 1 | |||||
|
Illuminator Resource Report Resource Website |
Illuminator (RRID:SCR_001019) | sequence analysis software, software resource, data analysis software, data processing software, software application | A sequence alignment program for the output from Illumina GA-II clonal sequencers. It uses an algorithm that indexes the reference sequence as a series of 8-mers and then matches the genomic reads to the 8-mer index, in a mutation-tolerant way permitting identification of single-nucleotide substitutions and indels. | sequence analysis software, sequence alignment, software, mutation detection, illumina, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Leeds; West Yorkshire; United Kingdom |
PMID:21621601 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:illuminator, OMICS_02165 | https://bio.tools/illuminator | SCR_001019 | 2026-08-06 09:25:19 | 0 | |||||||
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Visualization and Analysis of Networks containing Experimental Data (VANTED) Resource Report Resource Website 10+ mentions |
Visualization and Analysis of Networks containing Experimental Data (VANTED) (RRID:SCR_001138) | VANTED | software resource, data analysis software, data processing software, data visualization software, software application | Software tool for extendable network visualization and analysis for the life sciences. It is Java-based and allows users to create, edit and map data onto existing or new networks. Experimental datasets can be visualized on network elements as graphical charts to show time series data or data of different treatments, as well as environmental conditions in the context of the underlying biological processes. Users can utilize built-in statistical algorithms to evaluate mapped data. | binary executable, simulation software, signal processing software, java, network visualization, statistical analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:23140568 | Open source | biotools:vanted, nif-0000-00373 | https://bitbucket.org/vanted-dev/vanted/src, https://bio.tools/vanted | http://vanted.ipk-gatersleben.de/ | SCR_001138 | Visualization and Analysis of Networks containing Experimental Data, VANTED v2 | 2026-08-06 09:25:20 | 14 | ||||
|
NetNGlyc Resource Report Resource Website 1000+ mentions |
NetNGlyc (RRID:SCR_001570) | NetNGlyc | software resource, service resource, production service resource, data analysis service, software application, analysis service resource | Server that predicts N-Glycosylation sites in human proteins using artificial neural networks that examine the sequence context of Asn-Xaa-Ser/Thr sequons. NetNGlyc 1.0 is also available as a stand-alone software package, with the same functionality as the service above. Ready-to-ship packages exist for the most common UNIX platforms. | predict, n-glycosylation site, human, protein, neural network, sequence, asn-xaa-ser/thr sequon, glycoprotein, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: CBS Prediction Servers |
Free, Freely available | nlx_153863, biotools:netnglyc | https://bio.tools/netnglyc | SCR_001570 | NetNGlyc Server | 2026-08-06 09:25:25 | 1753 | ||||||
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YinOYang Resource Report Resource Website 100+ mentions |
YinOYang (RRID:SCR_001605) | YinOYang | software resource, service resource, production service resource, data analysis service, software application, analysis service resource | Server that produces neural network predictions for O-beta-GlcNAc attachment sites in eukaryotic protein sequences. This server can also use NetPhos, to mark possible phosphorylated sites and hence identify Yin-Yang sites. YinOYang 1.2 is available as a stand-alone software package, with the same functionality. Ready-to-ship packages exist for the most common UNIX platforms. | neural network, prediction, o-beta-glcnac attachment site, protein sequence, protein, sequence, glycosylation site, proteome, post-translational modification, protein function, glycoprotein, bio.tools |
uses: NetPhos is listed by: bio.tools is listed by: Debian has parent organization: CBS Prediction Servers |
Danish National Research Foundation | PMID:11928486 | Free, Freely available | nlx_153865, biotools:yinoyang | https://bio.tools/yinoyang | SCR_001605 | 2026-08-06 09:25:25 | 111 | |||||
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Clustal Omega Resource Report Resource Website 5000+ mentions |
Clustal Omega (RRID:SCR_001591) | Clustal Omega, Clustalo | software resource, image analysis software, alignment software, service resource, data processing software, software application | Software package as multiple sequence alignment tool that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences. Accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/Clustal, GCG/MSF, RSF. | multiple, sequence, alignment, DNA, RNA, protein, generate, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Clustal W2 is related to: Clustal W2 is related to: Clustal 2 has parent organization: European Bioinformatics Institute has parent organization: University College Dublin; Dublin; Ireland |
Science Foundation Ireland | PMID:21988835 PMID:20439314 DOI:10.1038/msb.2011.75 |
Free, Available for download, Freely available | OMICS_00972, SCR_016062, biotools:clustalo, nlx_153836 | https://sources.debian.org/src/clustalo/, http://www.clustal.org/omega/, http://mobyle.pasteur.fr/cgi-bin/portal.py#forms::clustalO-multialign, https://bio.tools/clustalo, https://sources.debian.org/src/clustalo/ | SCR_001591 | 2026-08-06 09:25:27 | 9956 | |||||
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MatrixDB Resource Report Resource Website 50+ mentions |
MatrixDB (RRID:SCR_001727) | MatrixDB | service resource, production service resource, database, data or information resource | Freely available database focused on interactions established by extracellular proteins and polysaccharides, taking into account the multimeric nature of the extracellular proteins (e.g. collagens, laminins and thrombospondins are multimers). MatrixDB is an active member of the International Molecular Exchange (IMEx) consortium and has adopted the PSI-MI standards for annotating and exchanging interaction data. It includes interaction data extracted from the literature by manual curation, and offers access to relevant data involving extracellular proteins provided by the IMEx partner databases through the PSICQUIC webservice, as well as data from the Human Protein Reference Database. The database reports mammalian protein-protein and protein-carbohydrate interactions involving extracellular molecules. Interactions with lipids and cations are also reported. MatrixDB is focused on mammalian interactions, but aims to integrate interaction datasets of model organisms when available. MatrixDB provides direct links to databases recapitulating mutations in genes encoding extracellular proteins, to UniGene and to the Human Protein Atlas that shows expression and localization of proteins in a large variety of normal human tissues and cells. MatrixDB allows researchers to perform customized queries and to build tissue- and disease-specific interaction networks that can be visualized and analyzed with Cytoscape or Medusa. Statistics (2013): 2283 extracellular matrix interactions including 2095 protein-protein and 169 protein-glycosaminoglycan interactions. | extracellular, protein fragment, biomolecule, cation, cleavage, collagen, glycosaminoglycan, human, interaction, laminin, lipid, mammalian, matricryptin, matrikin, matrix, molecule, monomer, mulimerization, multimer, polysaccharide, protein, protein-carbohydrate interaction, protein-protein interaction, recognition, thrombospondin, interactome, extracellular protein, protein-polysaccharide interaction, extracellular interaction, molecular interaction, model organism, inorganic, small molecule-protein, small molecule, extracellular matrix protein, protein-glycosaminoglycan interaction, bio.tools, FASEB list |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: IMEx - The International Molecular Exchange Consortium is related to: Gene Ontology is related to: PSI-MI is related to: HPRD - Human Protein Reference Database is related to: Interaction Reference Index is related to: ConsensusPathDB is related to: IMEx - The International Molecular Exchange Consortium is related to: PSICQUIC Registry is related to: IntAct has parent organization: Claude Bernard University Lyon 1; Lyon; France |
European Union contract FP7-HEALTH-2007-223411 | PMID:20852260 PMID:19147664 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:matrixdb, r3d100010672, nif-0000-10226 | https://bio.tools/matrixdb, https://doi.org/10.17616/R3M03H | http://matrixdb.ibcp.fr/ | SCR_001727 | MatrixDB: Extracellular Matrix Interactions Database, Extracellular Matrix Interactions Database | 2026-08-06 09:25:30 | 86 | |||
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Biocatalogue - The Life Science Web Services Registry Resource Report Resource Website 1+ mentions |
Biocatalogue - The Life Science Web Services Registry (RRID:SCR_001679) | BioCatalogue | software resource, data access protocol, web service, data or information resource, database | Crowd-curated catalog of life sciences Web services with over 2400 service entries, thereby enabling users (people and programs) to discover and use these services easily. It provides a platform with several (standardized) interfaces and a suite of tools for registration of services by the community of users as well as empowers the community to extend and enhance the system. BioCatalogue provides a centralized biological web services market place which is accessible to the world as it is searchable and indexable to search engines. Additionally, it provides a quality of service standard for biological web services thereby enabling services to be classified and checked for availability, reliability and other quality measures. Primary goals: * Provide a single registration point for Web Service providers and a single search site for scientists and developers. * Providers, Expert curators and Users will provide oversight, monitor the catalog and provide high quality annotations for services. * BioCatalogue is a place where the community can find contacts and meet the experts and maintainers of these services. | biological, web, life science, programmatic access, bioinformatics, registry, annotation, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: MetaLocGramN is related to: myExperiment is related to: bioDBcore has parent organization: European Bioinformatics Institute has parent organization: University of Manchester; Manchester; United Kingdom |
European Union LHSG-CT-2004-512092; EMBO ASTF 338.00-2009 |
PMID:20484378 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:biocatalogue, nif-0000-10167 | https://bio.tools/biocatalogue | SCR_001679 | Biocatalog | 2026-08-06 09:25:26 | 7 | ||||
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PhosphoSitePlus: Protein Modification Site Resource Report Resource Website 500+ mentions |
PhosphoSitePlus: Protein Modification Site (RRID:SCR_001837) | PSP | portal, knowledge environment resource, data or information resource | A freely accessible on-line systems biology resource devoted to all aspects of protein modification, as well as other post-translational modifications. It provides valuable and unique tools for both cell biologists and mass spectroscopists. PhosphoSite is a human- and mouse-centric database. It includes features such as: viewing the locations of modified residues on molecular models; browsing and searching MS2 records by disease, tissue, and cell line; submitting lists of peptides to identify previously reported genes; searching by sub-cellular localization, treatment, tissues, cell types, cell lines and diseases, and protein types and protein domains; searching for experimentally-verified kinase substrates and viewing preferred substrate motifs; and viewing MS2 spectra for peptides and sites not previously published. | portal, mass spectroscopist, molecular model, mouse, post translational, subcellular localization, protein modification, post-translational modification, protein phosphorylation, protein structure, protein function, ubiquitinylation, acetylation, cellular component, cell type, visualization, data repository, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: Cytoscape is related to: ConsensusPathDB has parent organization: Cell Signaling Technology |
NCI ; NIAAA R44 AA014848; NIGMS R43 GM65768 |
PMID:22135298 | Free, Freely available | biotools:phosphositeplus, nif-0000-10399 | https://bio.tools/phosphositeplus | SCR_001837 | PhosphoSitePlus, PhosphoSite | 2026-08-06 09:25:32 | 903 | ||||
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asSeq Resource Report Resource Website 1+ mentions |
asSeq (RRID:SCR_001625) | asSeq | source code, software resource, data analysis software, data processing software, software application | Software that establishes a statistical framework for future developments of eQTL (expression quantitative trait locus) mapping methods using RNA-seq data (e.g., linkage-based eQTL mapping), and the joint study of multiple genetic markers and/or multiple genes. This R package has been submitted to R/bioconductor. It will be available on bioconductor soon. It is recommended to install this R package from bioconductor. You can also install this R package from the source code by yourself. Since the R package contains C code, a C complier is required for installation. With both R and appropriate c complier installed, this R package can be installed using the following command (in Mac Terminal window or Windows command window) R CMD INSTALL asSeq | r, rna-seq, expression quantitative trait locus, total read count, allele-specific expression, allele-specific gene expression, gene expression quantitative trait locus, rna isoform, gene expression, genetic marker, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Bioconductor has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:21838806 | Free, Available for download, Freely available | OMICS_01948, nlx_153893, biotools:asseq | https://bio.tools/asseq | SCR_001625 | 2026-08-06 09:25:25 | 6 | ||||||
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MetaBase Resource Report Resource Website 50+ mentions |
MetaBase (RRID:SCR_001762) | MB | database, wiki, narrative resource, data or information resource | User-contributed list of biological databases available on the internet. Currently there are 1,801 entries, each describing a different database. The databases are described in a semi-structured way by using templates and entries can carry various user comments and annotations. Entries can be searched, listed or browsed by category. The site uses the same MediaWiki technology that powers Wikipedia, The Mediawiki system allows users to participate on many different levels, ranging from authors and editors to curators and designers. MetaBase aims to be a flexible, user-driven (user-created) resource for the biological database community. The main focuses of MetaBase are: * As a basic requirement, MB contains a list of databases, URLs and descriptions of the most commonly used biological databases currently available on the internet. * The system should be flexible, allowing users to contribute, update and maintain the data in different ways. * In the future we aim to generate more communication between the database developer and user communities. | biological, mediawiki, biology, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Genome Research Foundation |
MKE - Ministry of Knowledge Economy | PMID:22139927 | Free, Freely available | biotools:metabase, nif-0000-10293 | https://bio.tools/metabase | http://biodatabase.org/index.php?title=Main_Page&oldid=8972 | SCR_001762 | MetaBase (MB) | 2026-08-06 09:25:30 | 81 | |||
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SPP Resource Report Resource Website 1+ mentions |
SPP (RRID:SCR_001790) | data analysis software, software application, software resource, data processing software | R analysis and processing package for Illumina platform Chip-Seq data. | chip seq data, illummina, r package, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
NHGRI U01HG004258; NIGMS R01GM082798; NCRR UL1RR024920 |
DOI:10.1038/nbt.1508 | Free, Available for download, Freely available | OMICS_00425, biotools:spp | https://bio.tools/spp | https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/spp-r-from-chip-seq | SCR_001790 | SPP Package | 2026-08-06 09:25:31 | 9 | ||||
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myExperiment Resource Report Resource Website 10+ mentions |
myExperiment (RRID:SCR_001795) | myExperiment | storage service resource, software resource, community building portal, service resource, data repository, data or information resource, data processing software, portal, software application, workflow software, database | Community repository and virtual research environment where scientists can safely publish their workflows and experiment plans, share them with groups and find and use those of others. Workflows, other digital objects and collections (called Packs) can be swapped, sorted and searched. It supports Linked data, has a SPARQL Endpoint and REST API and is based on an open source Ruby on Rails codebase. Scientific workflows in various formats can be uploaded. Specific support is provided for Taverna workflows for which the system displays relevant metadata, components and visual previews, that are retrieved directly from workflow files. Version history for workflows is collected. This feature allows the contributor to keep previous versions of the workflow available, when the latest one is uploaded. This brings additional benefit for the users by allowing them to view the development stages of the workflow towards its latest implementation. | workflow, pipeline, platform, component, data sharing, publish, digital object, experimental method, workflow management, virtual research environment, collaborative computing, taverna workflow workbench, bioinformatics, web service, bio.tools |
is listed by: FORCE11 is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Taverna is related to: Workflow4Ever is related to: Biocatalogue - The Life Science Web Services Registry has parent organization: University of Southampton; Southampton; United Kingdom has parent organization: University of Manchester; Manchester; United Kingdom has parent organization: University of Oxford; Oxford; United Kingdom |
JISC ; Microsoft Technical Computing Initiative ; EPSRC |
PMID:20501605 | Free, Freely available | nif-0000-10309, r3d100010473, biotools:myexperiment | https://www.force11.org/node/4638, https://bio.tools/myexperiment | SCR_001795 | my experiment | 2026-08-06 09:25:28 | 23 | ||||
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bioRxiv Resource Report Resource Website 1000+ mentions |
bioRxiv (RRID:SCR_003933) | bioRxiv | portal, community building portal, database, data or information resource | A free archive and distribution service for unpublished preprints in the life sciences allowing authors to make their findings immediately available to the scientific community and receive feedback on draft manuscripts before they are submitted to journals. An article may be posted prior to, or concurrently with, submission to a journal but should not be posted if it has already been published. Once an article is published in a journal, bioRxiv will update the preprint with a link to the published version. | preprint, life science, bio.tools, FASEB list |
is used by: PrePubMed is listed by: LabWorm is listed by: bio.tools is listed by: Debian is related to: Overleaf has parent organization: Cold Spring Harbor Laboratory |
Free, Acknowledgement requested, The community can contribute to this resource | nlx_158302, biotools:bioRxiv | https://bio.tools/bioRxiv | SCR_003933 | bioRxiv - the preprint server for biology | 2026-08-06 09:26:02 | 1246 | ||||||
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Git Resource Report Resource Website 50+ mentions |
Git (RRID:SCR_003932) | software application, version source control system, software development tool, software resource | A free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency. Git is easy to learn and has a tiny footprint with lightning fast performance. It outclasses SCM tools like Subversion, CVS, Perforce, and ClearCase with features like cheap local branching, convenient staging areas, and multiple workflows. | version control, distributed, bio.tools |
is used by: DataLad is used by: G-Node Data Infrastructure Services is listed by: bio.tools is listed by: Debian works with: git-annex |
GNU General Public License, v2 | nlx_158301, biotools:Git | https://bio.tools/Git | SCR_003932 | 2026-08-06 09:26:00 | 66 |
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