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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
VirusSeq Resource Report Resource Website 10+ mentions |
VirusSeq (RRID:SCR_005206) | VirusSeq | software resource | An algorithmic software tool for detecting known viruses and their integration sites using next-generation sequencing of human cancer tissue. VirusSeq takes FASTQ files (paired-end reads) as input. | next-generation sequencing, virus, integration site, cancer tissue, genome, rna-seq, whole genome sequencing, fastq, paired-end read, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Texas MD Anderson Cancer Center |
Cancer | OMICS_00227, biotools:virusseq | https://bio.tools/virusseq | SCR_005206 | 2026-09-19 12:50:49 | 23 | |||||||
|
MethPipe Resource Report Resource Website 100+ mentions |
MethPipe (RRID:SCR_005168) | MethPipe | software resource | A computational pipeline for analyzing bisulfite sequencing data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Southern California; Los Angeles; USA |
PMID:24324667 | biotools:methpipe, OMICS_00603 | https://bio.tools/methpipe | SCR_005168 | 2026-09-19 12:50:48 | 108 | |||||||
|
SnpEff Resource Report Resource Website 5000+ mentions |
SnpEff (RRID:SCR_005191) | SnpEff | software resource | Genetic variant annotation and effect prediction software toolbox that annotates and predicts effects of variants on genes (such as amino acid changes). By using standards, such as VCF, SnpEff makes it easy to integrate with other programs. | genome, genetic variant, annotation, effect, variant, gene, cancer variant, gatk, hgsv, single nucleotide polymorphisms, genome sequence, java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: GATK has parent organization: SourceForge has parent organization: Wayne State University; Michigan; USA works with: SnpSift |
Cancer | PMID:22728672 | Free, Freely available | biotools:snpeff, OMICS_00186 | https://bio.tools/snpeff, https://sources.debian.org/src/snpeff/ | SCR_005191 | SnpEff - Genetic variant annotation and effect prediction toolbox | 2026-09-19 12:50:49 | 5640 | ||||
|
SimRare Resource Report Resource Website 1+ mentions |
SimRare (RRID:SCR_005226) | SimRare | software resource | A stand-alone executable software with user-friendly graphical interface implemented in Python/C++ for rare variant association studies. It is designed as a unified simulation framework to provide an unbiased and easy manner to evaluate association methods, including novel methods, under a broad range of choice of biological contexts. It consists of three modules, variant data simulator, genotype/phenotype generator and association method evaluator. SimRare generates variant data for gene regions using forward-time simulation which incorporates realistic population demographic and evolutionary scenarios. For phenotype data it is capable of generating both case-control and quantitative traits. The phenotypic effects of variants can be detrimental, protective or non-causal. SimRare has a graphical user interface which allows for easy entry of genetic and phenotypic parameters. Simulated data can be written into external files in a standard format. For novel association method implemented in R it can be imported into SimRare, which has been equipped built in functions to evaluate performance of new method and visually compare it with currently available ones in an unbiased manner. | statistical genetics, simulation framework, gui, association test, sequencing, rare variant, python, c++, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code has parent organization: Baylor University; Texas; USA |
PMID:22914216 | Acknowledgement requested, GNU General Public License, v3 | OMICS_00257, biotools:simrare | https://bio.tools/simrare | SCR_005226 | SimRare - A program to generate and analyze sequence-based data for rare variant association studies of quantitative and qualitative traits | 2026-09-19 12:50:49 | 2 | |||||
|
PHAge Search Tool Resource Report Resource Website 100+ mentions |
PHAge Search Tool (RRID:SCR_005184) | PHAST | analysis service resource, data analysis service, data or information resource, data set, production service resource, service resource | A web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. It accepts either raw DNA sequence data or partially annotated GenBank formatted data and rapidly performs a number of database comparisons as well as phage cornerstone feature identification steps to locate, annotate and display prophage sequences and prophage features. Relative to other prophage identification tools, PHAST is up to 40 times faster and up to 15% more sensitive. It is also able to process and annotate both raw DNA sequence data and Genbank files, provide richly annotated tables on prophage features and prophage quality and distinguish between intact and incomplete prophage. PHAST also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and linear genomic views. Databases available for download include Virus DB, Prophage and virus DB, Bacteria DB, and PHAST result DB. Pre-calculated genomes for viewing are also available. | prophage sequence, genome, prophage, sequence, bacterial genome, plasmid, dna sequence, graph, phage, annotate, virus, nucleotide sequence, fasta, annotated genome, genbank, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Alberta; Alberta; Canada |
PMID:21672955 | Acknowledgement requested | biotools:phast, OMICS_00180 | https://bio.tools/phast | SCR_005184 | PHAST - PHAge Search Tool | 2026-09-19 12:50:49 | 243 | |||||
|
GEPAT Resource Report Resource Website 1+ mentions |
GEPAT (RRID:SCR_003597) | GEPAT | software resource | A web-based software tool offering an integrated analysis of transcriptome data under genomic, proteomic and metabolic context. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:17543125 | OMICS_00765, biotools:gepat | https://bio.tools/gepat | SCR_003597 | Genome Expression Pathway Analysis Tool | 2026-09-19 12:50:23 | 2 | ||||||
|
J-Express Resource Report Resource Website 50+ mentions |
J-Express (RRID:SCR_003609) | J-Express | software resource | Gene expression analysis software using Java. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is parent organization of: Mini Analysis Guide for Microarrays |
PMID:11301307 | Acknowledgement requested | biotools:j-express, OMICS_00767 | https://bio.tools/j-express | SCR_003609 | J-Express: Gene expression analysis software | 2026-09-19 12:50:23 | 87 | |||||
|
bioRxiv Resource Report Resource Website 1000+ mentions |
bioRxiv (RRID:SCR_003933) | bioRxiv | community building portal, data or information resource, database, portal | 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 | biotools:bioRxiv, nlx_158302 | https://bio.tools/bioRxiv | SCR_003933 | bioRxiv - the preprint server for biology | 2026-09-19 12:50:29 | 1368 | ||||||
|
Git Resource Report Resource Website 50+ mentions |
Git (RRID:SCR_003932) | software application, software development tool, software resource, version source control system | 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 | 2026-09-19 12:50:29 | 73 | ||||||||
|
Quantitative Enrichment of Sequence Tags Resource Report Resource Website 10+ mentions |
Quantitative Enrichment of Sequence Tags (RRID:SCR_004065) | QuEST | software resource | A Kernel Density Estimator-based package for analysis of massively parallel sequencing data from chromatin immunoprecipitation (ChIP-seq) experiments. | genome-wide, transcription factor binding site, chip-seq, transcription factor, binding site, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: Stanford University; Stanford; California |
PMID:19160518 | OMICS_00458, biotools:quest | https://bio.tools/quest | SCR_004065 | Quantitative Enrichment of Sequence Tags: QuEST | 2026-09-19 12:50:32 | 49 | ||||||
|
Pash 3.0 Resource Report Resource Website 1+ mentions |
Pash 3.0 (RRID:SCR_004078) | Pash 3.0 | software resource | Performs sequence comparison and read mapping and can be employed as a module within diverse configurable analysis pipelines, including ChIP-Seq and methylome mapping by whole-genome bisulfite sequencing. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:21092284 | biotools:pash, OMICS_00586 | https://bio.tools/pash | SCR_004078 | 2026-09-19 12:50:32 | 1 | |||||||
|
EpiGRAPH Resource Report Resource Website 10+ mentions |
EpiGRAPH (RRID:SCR_004326) | EpiGRAPH | software resource | A software for genome and epigenome analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00633, biotools:epigraph | https://bio.tools/epigraph | SCR_004326 | 2026-09-19 12:50:36 | 18 | |||||||
|
PubChem Resource Report Resource Website 10000+ mentions |
PubChem (RRID:SCR_004284) | data or information resource, data repository, database, service resource, storage service resource | Collection of information about chemical structures and biological properties of small molecules and siRNA reagents hosted by the National Center for Biotechnology Information (NCBI). | collection, information, data, chemical, structure, biological, property, small, molecule, siRNA reagent, bio.tools |
uses: ChEMBL is used by: NIF Data Federation is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: GEROprotectors 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: NCBI Structure is related to: Molecular Libraries Program is related to: NIH Data Sharing Repositories is related to: PubChem BioAssay has parent organization: NCBI is parent organization of: PubChem Substance works with: MiMeDB |
NLM | PMID:21418625 PMID:21272340 PMID:20970519 PMID:20298522 PMID:19825798 |
Free, Freely Available | biotools:pubchem, nlx_42691, nlx_29861, r3d100010538, OMICS_01587 | https://bio.tools/pubchem, https://doi.org/10.17616/R3GW37 | SCR_004284 | 2026-09-19 12:50:35 | 15598 | ||||||
|
InsertionMapper Resource Report Resource Website |
InsertionMapper (RRID:SCR_004163) | InsertionMapper | software resource | A pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data. It consists of four independently working modules: Data Preprocessing, Database Modeling, Dimension Deconvolution and Element Mapping. This pipeline tool is applicable to scenarios requiring analysis of the tremendous output of short reads produced in NGS sequencing experiments of targeted genome sequences. | high throughput sequencing, dna sequence, next generation sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Montclair State University; New Jersey; USA |
PMID:24090499 | Acknowledgement requested, GNU General Public License | OMICS_01547, biotools:insertionmapper | https://bio.tools/insertionmapper | SCR_004163 | 2026-09-19 12:50:34 | 0 | ||||||
|
bcbio-nextgen Resource Report Resource Website 100+ mentions |
bcbio-nextgen (RRID:SCR_004316) | bcbio-nextgen | software resource | A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:bcbio-nextgen, OMICS_01121, BioTools:bcbio-nextgen | https://github.com/chapmanb/bcbb/blob/master/nextgen/README.md, https://bio.tools/bcbio-nextgen, https://bio.tools/bcbio-nextgen | SCR_004316 | 2026-09-19 12:50:36 | 165 | |||||||
|
PDBe - Protein Data Bank in Europe Resource Report Resource Website 50+ mentions |
PDBe - Protein Data Bank in Europe (RRID:SCR_004312) | PDBe | data or information resource, data repository, database, service resource, storage service resource | The European resource for the collection, organization and dissemination of data on biological macromolecular structures. In collaboration with the other worldwide Protein Data Bank (wwPDB) partners - the Research Collaboratory for Structural Bioinformatics (RCSB) and BioMagResBank (BMRB) in the USA and the Protein Data Bank of Japan (PDBj) - they work to collate, maintain and provide access to the global repository of macromolecular structure data. The main objectives of the work at PDBe are: * to provide an integrated resource of high-quality macromolecular structures and related data and make it available to the biomedical community via intuitive user interfaces. * to maintain in-house expertise in all the major structure-determination techniques (X-ray, NMR and EM) in order to stay abreast of technical and methodological developments in these fields, and to work with the community on issues of mutual interest (such as data representation, harvesting, formats and standards, or validation of structural data). * to provide high-quality deposition and annotation facilities for structural data as one of the wwPDB deposition sites. Several sophisticated tools are also available for the structural analysis of macromolecules. | x-ray, nmr, cryo-em, hybrid method, dna, protein, rna, sugar, ligand, virus, compound, fold, enzyme, 3d spatial image, structure, macromolecule, protein-protein interaction, gold standard, bio.tools |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: DNA DataBank of Japan (DDBJ) is related to: EMDataResource.org is related to: Worldwide Protein Data Bank (wwPDB) is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: DNA DataBank of Japan (DDBJ) is related to: Worldwide Protein Data Bank (wwPDB) is related to: PDBj - Protein Data Bank Japan is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: European Bioinformatics Institute is parent organization of: Electron Microscopy Data Bank at PDBe (MSD-EBI) works with: MOLEonline |
European Molecular Biology Laboratory; Heidelberg; Germany ; Wellcome Trust ; BBSRC ; NIH ; European Union ; MRC ; CCP4 |
PMID:21045060 PMID:21460450 PMID:19858099 |
r3d100012791, biotools:pdbe, nlx_32372 | https://bio.tools/pdbe, https://doi.org/10.17616/R3J226 | SCR_004312 | Protein DataBank Europe, Protein DataBank in Europe, PDBe, Protein Data Bank in Europe, Protein Data Bank Europe, Macromolecular Structure Database | 2026-09-19 12:50:35 | 55 | |||||
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NeuroMatic Resource Report Resource Website 100+ mentions |
NeuroMatic (RRID:SCR_004186) | data analysis software, data processing software, software application, software resource | NeuroMatic is a collection of Igor Pro functions for analyzing electrophysiological data. By allowing users to organize their data into Sets and Groups, NeuroMatic makes it relatively easy to compute transformations and statistical analyses on their data, including scaling, alignment averaging, baseline subtraction, spike detection, stationarity analysis, rise-time computations, etc. Being open source and modular designed, NeuroMatic also allows users to develop their own analysis functions that can be easily incorporated into NeuroMatic's framework. Note, if you have reached this page in search of a freeware tool for neuronal reconstructions, you are more likely to be interested in Neuromantic, a software package that sounds like NeuroMatic, but is not quite the same. Features of NeuroMatic Include * Sorting, Scaling, Averaging, Interpolation * Max / Min / Mean / Level / Rise Time / FWHM / Slope Measurements * Stability / Stationarity Analysis * Event Detection * Waveform Template Matching * Spike Raster Plots * Interspike-Interval and Peri-Stimulus Time (PST) Histograms * Compact Easy-to-Use Interface * Modular design as a basis for your own procedures * Extra space for your own buttons and controls * Import functions for Axograph and Pclamp data * Automatic macro generation for batch processing Supporting Agencies: MRC, Wellcome Trust Spike, Event, Fit, NClamp, Acquisition, spike train, EPSP, IPSP, IPSC, EPSC | epsc, epsp, event, fit, acquisition, data management, ipsc, ipsp, nclamp, software, spike, spike train, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University College London; London; United Kingdom |
PMID:29670519 | nif-0000-00073, biotools:neuromatic | https://bio.tools/neuromatic | SCR_004186 | NeuroMatic | 2026-09-19 12:50:34 | 315 | |||||||
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TagDust Resource Report Resource Website 50+ mentions |
TagDust (RRID:SCR_004175) | TagDust | software resource | A program to eliminate artifactual reads from next-generation sequencing data sets. | unix/linux, bio.tools, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:19737799 | biotools:tagdust, OMICS_01095, biotools:nexalign | https://bio.tools/tagdust, https://bio.tools/nexalign | SCR_004175 | 2026-09-19 12:50:34 | 55 | |||||||
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RatMine Resource Report Resource Website 1+ mentions |
RatMine (RRID:SCR_004190) | analysis service resource, data access protocol, data analysis service, data or information resource, database, production service resource, service resource, software resource, web service | RatMine integrates data from RGD, UniProtKB, NCBI, KEGG and other sources to form a web-based data warehouse and tool set tailored for rat based data research. Search RatMine by entering names, identifiers, or keywords for genes, proteins, pathways, papers, etc. Additionally, we support programmatic access to our data through Application Programming Interface - choose from Perl or Java API. RatMine is a data warehouse that integrates many diverse biological data sets. The main focus is R. norvegicus genomics and proteomics. By integrating such data into one place it is possible to construct queries across domains of biological knowledge. The RatMine user interface is designed to go beyond simply looking up an identifier and viewing a report page. Some of the features include: * Quick Search is available just like on other sites, type in an identifier to see a report page. * Template queries are ''canned'' queries that provide a simple form to perform a specific task. You can create your own templates if you log in. * Lists lets you operate on whole lists of data at once. You can upload lists or save them from results tables. We also create useful public lists for everyone to use. * MyMine lets you create an account to save your own queries, bags and templates, as well as marking public templates as favorites. | disease, interaction, proteins, single nucleotide, gene ontology, mammalian phenotype, publication, genomics, pathway, quantitative trait loci, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Medical College of Wisconsin; Wisconsin; USA |
biotools:RatMine, nlx_21635 | https://bio.tools/RatMine | SCR_004190 | 2026-09-19 12:50:34 | 5 | |||||||||
|
Artemis: Genome Browser and Annotation Tool Resource Report Resource Website 100+ mentions |
Artemis: Genome Browser and Annotation Tool (RRID:SCR_004267) | Artemis | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Free genome browser and annotation tool that allows visualization of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation. Artemis is free software and is distributed under the terms of the GNU General Public License. Artemis is written in Java, and is available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK database entries or sequence in FASTA, indexed FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format. | training tool, genome browser, gene annotation, java, bio.tools |
is listed by: OMICtools is listed by: 3DVC is listed by: Debian is listed by: bio.tools is related to: DNAPlotter has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom works with: Alien-hunter |
Wellcome Trust | PMID:11120685 DOI:10.1093/bioinformatics/btr703 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_28554, OMICS_00903, biotools:artemis | https://bio.tools/artemis, https://sources.debian.org/src/art-nextgen-simulation-tools/ | SCR_004267 | 2026-09-19 12:50:35 | 422 |
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