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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Pseudomonas Genome Database Resource Report Resource Website 100+ mentions |
Pseudomonas Genome Database (RRID:SCR_006590) | PseudoCAP | service resource, production service resource, data analysis service, data or information resource, analysis service resource, database | Database of peer-reviewed, continually updated annotation for the Pseudomonas aeruginosa PAO1 reference strain genome expanded to include all Pseudomonas species to facilitate cross-strain and cross-species genome comparisons with high quality comparative genomics. The database contains robust assessment of orthologs, a novel ortholog clustering method, and incorporates five views of the data at the sequence and annotation levels (Gbrowse, Mauve and custom views) to facilitate genome comparisons. Other features include more accurate protein subcellular localization predictions and a user-friendly, Boolean searchable log file of updates for the reference strain PAO1. The current annotation is updated using recent research literature and peer-reviewed submissions by a worldwide community of PseudoCAP (Pseudomonas aeruginosa Community Annotation Project) participating researchers. If you are interested in participating, you are invited to get involved. Many annotations, DNA sequences, Orthologs, Intergenic DNA, and Protein sequences are available for download. | gene, genome, annotation, localization, prokaryote, pseudomonas aeruginosa, sequence, subcellular, cystic fibrosis, ortholog, annotation, dna sequence, intergenic dna, protein sequence, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: Debian is listed by: bio.tools is related to: AmiGO has parent organization: Simon Fraser University; British Columbia; Canada has parent organization: University of British Columbia; British Columbia; Canada |
Cystic Fibrosis Foundation Therapeutics Inc | PMID:18978025 | nif-0000-03369, r3d100012086, biotools:pseudomonas_genome_database | https://bio.tools/pseudomonas_genome_database, https://doi.org/10.17616/R3935H | SCR_006590 | Pseudomonas Genome Database - Improving Disease Treatment Through Genome Research | 2026-08-06 09:26:38 | 489 | |||||
|
BAR Resource Report Resource Website 10+ mentions |
BAR (RRID:SCR_006748) | BAR | data set, service resource, production service resource, data analysis service, data or information resource, analysis service resource | Web-based tools for working with functional genomics and other data, including Gene Expression and Protein Tools, Molecular Markers and Mapping Tools, and Other Genomic Tools. Most are designed with the plant (mainly Arabidopsis) researcher in mind, but a couple of them can be useful to the wider research community, e.g. Mouse eFP Browser or BlastDigester. The associated paper for most tools is available. | gene expression, protein, molecular marker, mapping, tool, genomic, genomics, functional genomics, interaction, molecular interaction, protein-protein interaction, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: PSICQUIC Registry has parent organization: University of Toronto; Ontario; Canada |
Canada Foundation for Innovation ; Genome Canada |
nlx_152191, biotools:bioanalres_bar | https://bio.tools/bioanalres_bar | SCR_006748 | Bio-Analytic Resource for Plant Biology, Bio-Analytic Resource, Bio-Analytic Resource - the BAR | 2026-08-06 09:26:40 | 45 | ||||||
|
MaizeGDB Resource Report Resource Website 500+ mentions |
MaizeGDB (RRID:SCR_006600) | MaizeGDB | storage service resource, topical portal, service resource, organism-related portal, production service resource, data repository, data analysis service, data or information resource, portal, analysis service resource, database | Collection of data related to crop plant and model organism Zea mays. Used to synthesize, display, and provide access to maize genomics and genetics data, prioritizing mutant and phenotype data and tools, structural and genetic map sets, and gene models and to provide support services to the community of maize researchers. Data stored at MaizeGDB was inherited from the MaizeDB and ZmDB projects. Sequence data are from GenBank. Data are searchable by phenotype, traits, Pests, Gel Pattern, and Mutant Images. | zea mays, corn, model organism, genome, locus, metabolic pathway, genetics, genomics, sequence, gene product, function, literature reference, phenotype, trait, pest, gel pattern, mutant, blast, gene, image, corn, genotype-environment interaction, gene mapping, plant genome mapping, plant genome, gold standard, bio.tools, FASEB list |
is listed by: re3data.org is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: GenBank has parent organization: University of Maryland; Maryland; USA works with: Maize Database of Images and Genomes |
USDA ; USDA/ARS ; NSF ; National Corn Growers Association |
PMID:21624896 PMID:18769488 PMID:15888678 PMID:14681441 |
Free, Freely available, Acknowledgement requested, The community can contribute to this resource | OMICS_01655, biotools:MaizeDIG, nif-0000-03096, r3d100010795 | https://bio.tools/MaizeDIG, https://doi.org/10.17616/R3V32B | SCR_006600 | Maize Genetics and Genomics Database, MaizeGDB, MaizeGDB Locus | 2026-08-06 09:26:38 | 806 | ||||
|
The Human Protein Atlas Resource Report Resource Website 5000+ mentions |
The Human Protein Atlas (RRID:SCR_006710) | HPA | knowledge base, data or information resource | Open access resource for human proteins. Used to search for specific genes or proteins or explore different resources, each focusing on particular aspect of the genome-wide analysis of the human proteins: Tissue, Brain, Single Cell, Subcellular, Cancer, Blood, Cell line, Structure and Interaction. Swedish-based program to map all human proteins in cells, tissues, and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics, and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome. | human proteins, human proteome exploration, genome-wide analysis of human proteins, Tissue, Brain, Single Cell, Subcellular, Cancer, Blood, Cell line, Structure and Interaction, bio.tools, FASEB list |
is used by: MitoMiner is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: aGEM has parent organization: HUPO Antibody Initiative |
Cancer, Tumor, Breast cancer, Colorectal cancer, Lung cancer, Prostate cancer, Normal | Knut and Alice Wallenberg Foundation | PMID:21139605 PMID:16127175 PMID:18669619 PMID:18853439 |
Public, Free, For informational purposes, Non-commercial, Acknowledgement required | nif-0000-00204, biotools:proteinatlas | https://bio.tools/proteinatlas | SCR_006710 | HPA antibody, Human Protein Atlas | 2026-08-06 09:26:40 | 7492 | |||
|
Cistrome Resource Report Resource Website 10+ mentions |
Cistrome (RRID:SCR_000242) | data access protocol, web service, software resource | Web based integrative platform for transcriptional regulation studies. | Transcriptional, regulation, Chip, data, analysis, genome, gene, expression, motif, mining, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Galaxy has parent organization: Harvard University; Cambridge; United States |
Dana-Farber Cancer Institute High Tech and Campaign Technology Fund ; National Basic Research Program of China ; NHGRI HG004069; NIDDK DK074967; NIDDK DK062434 |
PMID:21859476 | Free, Freely available | SCR_017663, biotools:cistrome, OMICS_02173 | http://cistrome.org/ap/root, https://bio.tools/cistrome | SCR_000242 | Galaxy Cistrome | 2026-08-06 09:25:08 | 16 | |||||
|
CovalentDock Cloud Resource Report Resource Website |
CovalentDock Cloud (RRID:SCR_000126) | CovalentDock Cloud | data access protocol, web service, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Web service that is used by researchers and scientists to perform protein-ligand covalent docking. This form allows for the formation of covalent linkages between the ligand and the receptor. | protein ligand covalent docking, ligand, receptor, covalent linkage, data analysis service, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23034731 | THIS RESOURCE IS NO LONGER IN SERVICE | covalentdock_cloud, OMICS_01597 | https://bio.tools/covalentdock_cloud | SCR_000126 | 2026-08-06 09:25:07 | 0 | ||||||
|
cn.FARMS Resource Report Resource Website |
cn.FARMS (RRID:SCR_000289) | cn.FARMS | software resource, data analysis software, software toolkit, data processing software, software application | Software R package for copy number variation analysis that allows analysis of the most common Affymetrix (250K-SNP6.0) array types and supports high-performance computing using snow and ff. | copy number variation analysis, copy number variation, microarray, affymetrix, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:21486749 | Free, Available for download, Freely available | biotools:cn.farms, OMICS_02060 | https://bio.tools/cn.farms | SCR_000289 | cn.farms - factor analysis for copy number estimation | 2026-08-06 09:25:09 | 0 | |||||
|
Fusion Analyser Resource Report Resource Website |
Fusion Analyser (RRID:SCR_000059) | data analysis software, software application, software resource, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16, 2023. Software used to detect gene fusions from paired-end RNA-Seq data. | gene fusion, rna-seq, paired-end rna-seq data, fusion event, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:22570408 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01347, biotools:fusionanalyser | https://bio.tools/fusionanalyser | SCR_000059 | FusionAnalyser | 2026-08-06 09:25:06 | 0 | ||||||
|
CorMut Resource Report Resource Website |
CorMut (RRID:SCR_000053) | sequence analysis software, software resource, data analysis software, data processing software, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Software package for computing correlated mutations based on selection pressure. Three methods are provided for detecting correlated mutations, including conditional selection pressure, mutual information and Jaccard index. The computation consists of two steps: First, the positive selection sites are detected; second, the mutation correlations are computed among the positive selection sites. Note that the first step is optional. Meanwhile, CorMut facilitates the comparison of the correlated mutations between two conditions by the means of correlated mutation network. | sequencing, correlated mutation, selection pressure, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: CRAN has parent organization: Bioconductor |
PMID:24681904 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_03636, biotools:cormut | https://bio.tools/cormut | SCR_000053 | CorMut - Detect the correlated mutations based on selection pressure | 2026-08-06 09:25:06 | 0 | ||||||
|
RNAcontext Resource Report Resource Website 1+ mentions |
RNAcontext (RRID:SCR_000179) | RNAcontext | software resource, data access protocol, service resource, production service resource, web service, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Motif finding software suited for using large-scale RNA-binding affinity datasets to determine the relative binding preferences of RNA-binding proteins (RBPs) for a wide range of RNA sequences and structures. The tool is also implemented in a website. | rna-binding protein, motif, rna sequence, rna structure, rna, binding preference, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Toronto; Ontario; Canada |
PMID:20617199 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02253, biotools:rnacontext | https://bio.tools/rnacontext | SCR_000179 | 2026-08-06 09:25:08 | 2 | ||||||
|
nmrML Resource Report Resource Website 1+ mentions |
nmrML (RRID:SCR_000467) | nmrML | markup language, interchange format, data or information resource, standard specification, narrative resource | An open mark-up language for NMR data. | nuclear magnetic resonance, bio.tools |
is listed by: bio.tools is listed by: Debian is parent organization of: nmrCV |
nlx_157309, biotools:nmrml_converter | https://bio.tools/nmrml_converter | SCR_000467 | 2026-08-06 09:25:11 | 9 | ||||||||
|
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 | |||||||
|
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 | |||||
|
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 | |||||
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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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