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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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QuickNII Resource Report Resource Website 10+ mentions |
QuickNII (RRID:SCR_016854) | QuickNII | data processing software, registration software, software resource, software application, image processing software, image analysis software | Histological brain section series aligner to volumetric atlases. Software tool for user guided affine registration (anchoring) of 2D experimental image data, typically high resolution microscopic images, to 3D atlas reference space, facilitating data integration through standardized coordinate systems. Part of the QUINT workflow. | section, series, aligner, volumetric, 3D, atlas, reference, space, anchoring, data, image, microscopic, standardized, coordinate, system, bio.tools |
is used by: BICCN is listed by: Debian is listed by: bio.tools is listed by: EBRAINS is related to: LocaliZoom is related to: Allen Institute for Brain Science has parent organization: University of Oslo; Oslo; Norway |
European Union Horizon 2020 Framework Programme for Research and Innovation under the Framework Partnership Agreement | PMID:31141518 | Free, Available for download, Freely available | biotools:QuickNII | https://quicknii.readthedocs.io; https://bio.tools/QuickNII, https://github.com/Tevemadar/QuickNII | SCR_016854 | 2026-08-04 09:44:00 | 37 | |||||
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Heatmapper Resource Report Resource Website 100+ mentions |
Heatmapper (RRID:SCR_016974) | data processing software, web service, software resource, data access protocol, software application | Software tool to create and provide heat maps through a graphical interface. Allows to create an expression, pairwise comparison, image overlay, geomap, and geocoordinate heat maps for different data types and applications. Used to interactively visualize data. | expression, based, heat, map, pairwise, comparison, distance, correlation, image, overlay, latitude, longitude, geomap, geopolitical, geocoordinate, choropleth, data, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing has parent organization: Wishart Research Group is provided by: University of Alberta; Alberta; Canada |
Canadian Institutes of Health Research ; Genome Alberta |
PMID:27190236 | Freely available, Free, Acknowledgement requested | OMICS_12077, biotools:heatmapper | http://www.heatmapper.ca, https://github.com/WishartLab/heatmapper, https://bio.tools/heatmapper | SCR_016974 | Heatmapper, HeatMapper, heat mapper | 2026-08-04 09:44:01 | 131 | |||||
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Gigwa Resource Report Resource Website 1+ mentions |
Gigwa (RRID:SCR_017080) | data processing software, data analysis software, analysis service resource, data management software, data distribution software, web service, software resource, application programming interface, software application, data access protocol, production service resource, service resource, biomaterial analysis service, material analysis service | Web tool to explore genotyping metdata by filtering it on basis of variant features, including functional annotations and matching genotype patterns. May be deployed on workstation or as data portal. Allows to feed MongoDB database with VCF, PLINK or HapMap files and provides interface to filter data in real time. Used to export filtered data into formats and features connectivity with online genomic tools and with standalone software such as FlapJack or IGV. Gigwa hosted datasets are interoperable via two standard REST APIs such GA4GH and BrAPI. | metadata, genotyping, filter, variant, functional, annotation, pattern, bio.tools |
is listed by: Debian is listed by: bio.tools |
UMR DIADE and Agropolis Fundation | PMID:27267926 | Free, Freely available | biotools:Gigwa | https://github.com/SouthGreenPlatform/Gigwa2, https://bio.tools/Gigwa | SCR_017080 | GIGWA, GIGWA2, Genotype Investigator for Genome Wide Analysis | 2026-08-04 09:44:06 | 2 | |||||
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CATALYST Resource Report Resource Website 100+ mentions |
CATALYST (RRID:SCR_017127) | data processing software, data analysis software, software resource, software application, software toolkit | Software R package to provide pipeline for preprocessing of cytometry data, including normalization using bead standards, single cell deconvolution, and bead based compensation. | preprocessing, cytometry, data, normalization, bead, standard, single, cell, deconvulsion, compensation, bio.tools |
uses: CATALYSTLite is listed by: Bioconductor is listed by: bio.tools is listed by: Debian |
Swiss National Science Foundation ; SNSF Assistant Professorship grant ; PhosphonetPPM and MetastasiX SystemsX grant ; NIDDK UC4 DK108132; European Research Council ; Roche Postdoctoral Fellowship |
PMID:29605184 | Free, Available for download, Freely available | biotools:catalyst | https://github.com/HelenaLC/CATALYST, https://bio.tools/catalyst | SCR_017127 | Cytometry dATa anALYSis Tools | 2026-08-04 09:44:05 | 223 | |||||
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SwiftOrtho Resource Report Resource Website 1+ mentions |
SwiftOrtho (RRID:SCR_017122) | data processing software, software application, software resource, data analysis software | Software tool for orthology analysis to identify orthologs, paralogs and co orthologs for genomes. Used to perform homology classification across genomes of different species in large genomic datasets. | orthology, analysis, identify, ortholog, paralog, co ortholog, genome, homology, different, species, large, dataset, bio.tools |
uses: Python Programming Language is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1101/543223 | Free, Available for download, Freely available | OMICS_30890, biotools:SwiftOrtho | https://bio.tools/SwiftOrtho | SCR_017122 | 2026-08-04 09:44:04 | 4 | |||||||
|
Experimental Design Assistant Resource Report Resource Website 100+ mentions |
Experimental Design Assistant (RRID:SCR_017019) | EDA | web application, software resource, service resource | Web based tool to help in vivo researchers improve design, conduct, analysis and reporting of animal experiments.Provides automated feedback on proposed design and generates graphical summary that aids communication with colleagues, founders and regulatory authorities. Addresses causes of irreproducibility. | in vivo, design, conduct, analysis, reporting, animal, experiment, irreproducibility, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: NC3Rs |
PMID:28957312 | Free, Freely available | biotools:eda | https://bio.tools/eda | SCR_017019 | EDA, Experimental Design Assistant (EDA), Experimental Design Assistant | 2026-08-04 09:44:03 | 187 | |||||
|
ClustVis Resource Report Resource Website 500+ mentions Issue |
ClustVis (RRID:SCR_017133) | data analysis service, analysis service resource, web service, software resource, data access protocol, production service resource, service resource | Web user interface for visualizing clustering of multivariate data. Web server allows users to upload their own data and create Principal Component Analysis plots and heatmaps. | visualizing, clustering, multivariate, data, principal, component, analysis, plot, heatmap, bio.tools |
uses: Shiny uses: ggplot2 uses: pheatmap uses: RColorBrewer uses: FactoMineR is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: R Project for Statistical Computing has parent organization: University of Tartu; Tartu; Estonia |
Innovative Medicines Initiative Joint Undertaking ; European Union Seventh Framework Programme ; European Federation of Pharmaceutical Industries and Associations ; European Regional Development Fund ; Estonian Research Council ; European Commission ; EFPIA |
PMID:25969447 | biotools:clustvis, OMICS_08539 | https://github.com/taunometsalu/ClustVis, https://bio.tools/clustvis | SCR_017133 | 2026-08-04 09:44:05 | 798 | |||||||
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Comparative Metatranscriptomics Workflow Resource Report Resource Website 1+ mentions |
Comparative Metatranscriptomics Workflow (RRID:SCR_017109) | CoMW | data processing software, data analysis software, workflow, software resource, training material, sequence analysis software, software application, narrative resource, data or information resource | Software tool for standardized and validated workflow to functionally classify quality filtered mRNA reads from metatranscriptomic or total RNA studies generated using NGS short reads. Used for classification of these reads using assembled contigs to reference databases. | workflow, functionally, classify, mRNA, metatranscriptomic, RNA, next, generation, sequencing, NGS, short, read, assembly, contig, reference, database, bio.tools |
is listed by: bio.tools is listed by: Debian |
h2020 EU MicroArctic ITN | Free, Available for download, Freely available | biotools:comw | https://bio.tools/CoMW | SCR_017109 | 2026-08-04 09:44:04 | 3 | ||||||
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HaTSPiL Resource Report Resource Website 1+ mentions |
HaTSPiL (RRID:SCR_017059) | data processing software, data analysis software, software resource, sequence analysis software, software application | Software Python tool for high throughput sequencing analysis, focused on high reliability, modularity and customisability. | next, generation, sequencing, pipeline, metadata, analysis, mutation, barcoding, customisability, modularity, bio.tools |
uses: Python Programming Language is listed by: Debian is listed by: bio.tools has parent organization: Italian Institute for Genomic Medicine; Turin; Italy |
Free, Available for download, Freely available | biotools:HatSPiL | https://bio.tools/HaTSPiL | SCR_017059 | 2026-08-04 09:44:04 | 1 | ||||||||
|
PRSice Resource Report Resource Website 50+ mentions |
PRSice (RRID:SCR_017057) | data processing software, software application, software resource, data analysis software | Software R package for calculating, applying, evaluating and plotting results of polygenic risk scores analysis. Performs simulation study to estimate P value significance threshold for high resolution PRS studies and produces plots for inspection of results. Operating Unix/Linux. | polygenic, risk, score, calculating, applying, plotting, result, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
EU ; NIHR Biomedical Research Centre |
PMID:25550326 | Free, Available for download, Freely available | OMICS_23656, biotools:prsice | https://choishingwan.github.io/PRSice/, https://bio.tools/prsice | SCR_017057 | prsice, PRSice-2, Polygenic Risk Score software, PRSice1, PRSice2 | 2026-08-04 09:44:03 | 97 | |||||
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BinPacker Resource Report Resource Website 10+ mentions |
BinPacker (RRID:SCR_017038) | data processing software, software application, software resource, data analysis software | Software tool as de novo trascriptome assembler for RNA-Seq data. Used to assemble full length transcripts by remodeling problem as tracking set of trajectories of items over splicing graph. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux. | de novo, transcriptome, assembler, RNAseq, data, full, length, transcript, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
National Natural Science Foundation of China ; NSF 1553680; NCRR P20 RR01 6460; NIGMS P20 GM103429 |
PMID:26894997 | Free, Available for download, Freely available | OMICS_11199, biotools:binpacker | http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_1.0.tar.gz/download, http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_binary.tar.gz/download, https://bio.tools/binpacker | SCR_017038 | 2026-08-04 09:44:03 | 10 | ||||||
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PS-Plant Framework Resource Report Resource Website 1+ mentions |
PS-Plant Framework (RRID:SCR_017032) | PS-Plant | segmentation software, data processing software, code testing framework, data analysis software, time-series analysis software, software development tool, software resource, 3d time-series analysis software, software application, workflow software, image analysis software, image, 2d spatial image, 3d visualization software, data visualization software, data or information resource | Software tool as end to end software for data acquisition, processing, and result extraction of Arabidopsis thaliana growth. Framework uses photometric stereo based 3D imaging system with computer vision and deep learning for tracking and quantifying both plant growth and movement parameters. | photometric, 3D, imaging, tracking, plant, growth, arabidopsis, thaliana, leaf, angle, segmentation, machine, learning, near-infrared, (NIR), LED, photomorphogenesis, thermomorphogenesis, bio.tools |
uses: Python Programming Language is listed by: bio.tools is listed by: Debian |
BBSRC BB/N02334X/1; BBSRC BB/M025551/1; BBSRC BB/N005147/1 |
Free, Available for download, Freely available | biotools:PS-Plant | https://bio.tools/PS-Plant | SCR_017032 | 2026-08-04 09:44:03 | 1 | ||||||
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GBrowse Resource Report Resource Website 10+ mentions |
GBrowse (RRID:SCR_006829) | GBrowse | database, data or information resource | A database and interactive web site for manipulating and displaying annotations on genomes. Features include: detailed views of the genome; use of a variety of premade or personally made glyphs ; customizable order and appearance of tracks by administrators and end-users; search by annotation ID, name, or comment; support of third party annotation using GFF formats; DNA and GFF dumps; connectivity to different databases, including BioSQL and Chado; and a customizable plug-in architecture (e.g. run BLAST, find oligonucleotides, design primers, etc.). GBrowse is distributed as source code for Macintosh OS X, UNIX and Linux platforms, and as pre-packaged binaries for Windows machines. It can be installed using the standard Perl module build procedure, or automated using a network-based install script. In order to use the net installer, you will need to have Perl 5.8.6 or higher and the Apache web server installed. The wiki portion accepts data submissions. | genome, annotation, database, perl, virus, dna, protein, reference sequence, chromosome, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: WormBase is related to: FlyBase is related to: International HapMap Project has parent organization: Generic Model Organism Database Project has parent organization: Indiana University; Indiana; USA |
Howard Hughes Medical Institute ; NHGRI HG00739; NHGRI P41HG02223 |
PMID:19957275 PMID:18428797 PMID:12368253 PMID:21400697 PMID:20194461 PMID:19357095 DOI:10.1002/0471250953.bi0909s28 |
The community can contribute to this resource, Requires Perl 5.8.6 or higher and the Apache web server | OMICS_00910, biotools:gbrowse, nif-0000-30597 | http://gmod.org/wiki/GBrowse, https://bio.tools/gbrowse, https://sources.debian.org/src/gbrowse/ | SCR_006829 | Generic Genome Browser | 2026-08-04 09:41:41 | 43 | ||||
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SWISS-2DPAGE Resource Report Resource Website 1+ mentions |
SWISS-2DPAGE (RRID:SCR_006946) | database, data or information resource | A database of proteins identified by various 2-D PAGE and SDS-PAGE reference maps. Each SWISS-2DPAGE entry contains textual data on one protein, including mapping procedures, physiological and pathological information, experimental data (isoelectric point, molecular weight, amino acid composition, peptide masses) and bibliographical references. In addition to this textual data, SWISS-2DPAGE provides several 2-D PAGE and SDS-PAGE images showing the experimentally determined location of the protein, as well as a theoretical region computed from the sequence protein, indicating where the protein might be found in the gel. Using the database, users can locate these proteins on the 2-D PAGE maps or display the region of a 2-D PAGE map where one might expect to find a protein from UniProtKB/Swiss-Prot. | bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: SIB Swiss Institute of Bioinformatics has parent organization: University of Geneva; Geneva; Switzerland |
biotools:swiss-2dpage, nif-0000-03521 | https://bio.tools/swiss-2dpage | SCR_006946 | SWISS-2DPAGE | 2026-08-04 09:41:43 | 3 | ||||||||
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SCOP: Structural Classification of Proteins Resource Report Resource Website 50+ mentions |
SCOP: Structural Classification of Proteins (RRID:SCR_007039) | database, data or information resource | The Structural Classification of Proteins (SCOP) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships. Protein domains in SCOP are hierarchically classified into families, superfamilies, folds and classes. The continual accumulation of sequence and structural data allows more rigorous analysis and provides important information for understanding the protein world and its evolutionary repertoire. SCOP participates in a project that aims to rationalize and integrate the data on proteins held in several sequence and structure databases. As part of this project, starting with release 1.63, we have initiated a refinement of the SCOP classification, which introduces a number of changes mostly at the levels below superfamily. The pending SCOP reclassification will be carried out gradually through a number of future releases. In addition to the expanded set of static links to external resources, available at the level of domain entries, we have started modernization of the interface capabilities of SCOP allowing more dynamic links with other databases. | bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: IndelFR - Indel Flanking Region Database is related to: SUPFAM is related to: DOMMINO - Database Of MacroMolecular INteractiOns has parent organization: MRC Laboratory of Molecular Biology |
PMID:14681400 | nlx_94704, biotools:scop | https://bio.tools/scop | SCR_007039 | Structural Classification of Proteins database, SCOP database | 2026-08-04 09:41:44 | 98 | |||||||
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AgBase Resource Report Resource Website 100+ mentions |
AgBase (RRID:SCR_007547) | AgBase | database, data or information resource | A curated, open-source, web-accessible resource for functional analysis of agricultural plant and animal gene products. Our long-term goal is to serve the needs of the agricultural research communities by facilitating post-genome biology for agriculture researchers and for those researchers primarily using agricultural species as biomedical models. AgBase provides tools designed to assist with the analysis of proteomics data and tools to evaluate experimental datasets using the GO. Additional tools for sequence analysis are also provided. We use controlled vocabularies developed by the Gene Ontology (GO) Consortium to describe molecular function, biological process, and cellular component for genes and gene products in agricultural species. AgBase will also accept annotations from any interested party in the research communities. AgBase develops freely available tools for functional analysis, including tools for using GO. We appreciate any and all questions, comments, and suggestions. AgBase uses the NCBI Blast program for searches for similar sequences. And the Taxonomy Browser allows users to find the NCBI defined taxon ID for or taxon name for different organisms. | gene ontology, agricultural species, biological process, cellular component for genes, molecular function, protein identification, animals, plants, microbes, parasites, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: IntAct has parent organization: Mississippi State University; Mississippi; USA is parent organization of: GORetriever is parent organization of: GOSlimViewer is parent organization of: GOProfiler is parent organization of: GOanna |
Mississippi State University; Mississippi; USA ; USDA Agriculture and Food Research Initiative Competitive Grant 2011-67015-30332; National Research Initiative of the USDA Cooperative State Research Education and Extension Service 2007-35205-17941; NIGMS project 07111084; NSF EPS 0903787 |
PMID:21075795 | nif-0000-02537, biotools:agbase, r3d100012427 | https://bio.tools/agbase, https://doi.org/10.17616/R3P772 | SCR_007547 | 2026-08-04 09:41:52 | 111 | ||||||
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HubMed Resource Report Resource Website 1+ mentions |
HubMed (RRID:SCR_007296) | database, data or information resource | HubMed provides an interface to PubMed. Quick access to searches with a Firefox search plugin or a HubMed bookmarklet (drag to your browser''s bookmarks toolbar). Export citations in RIS, BibTeX, RDF and MODS formats, or directly to RefWorks. Unzip HubMed''s import filter into Endnote''s Filters folder for direct import into Endnote, or install the RIS Export plugin for direct import into ProCite, RefMan and older versions of Endnote. Use the Citation Finder to convert reference lists from PDFs into search results. Create lists of closely related papers using Rank Relations, then visualise and browse clusters of related papers using TouchGraph (requires Java). Graph occurrences of keywords in published papers over time. Tag and store annotated metadata for articles of interest. | bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: National Center for Integrative Biomedical Informatics |
nif-0000-00111, biotools:hubmed | https://bio.tools/hubmed | SCR_007296 | HubMed | 2026-08-04 09:41:48 | 8 | ||||||||
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CuticleDB Resource Report Resource Website 10+ mentions |
CuticleDB (RRID:SCR_007045) | cuticleDB | database, data or information resource | A relational database containing all structural proteins of Arthropod cuticle identified to date. Many come from direct sequencing of proteins isolated from cuticle and from sequences from cDNAs that share common features with these authentic cuticular proteins. It also includes proteins from the five sequenced genomes where manual annotation has been applied to cuticular proteins: Anopheles gambiae, Apis mellifera, Bombyx mori, Drosophila melanogaster, and Nasonia vitripennis. Some sequences were confirmed as authentic cuticular proteins because protein sequencing revealed that they were present in cuticle; others were identified by sequence homology and other criteria. Entries provides information about whether sequences are putative or authentic cuticular proteins. CuticleDB was primarily designed to contain correct and full annotation of cuticular protein data. The database will be of help to future genome annotators. Users will be able to test hypotheses for the existence of known and also of yet unknown motifs in cuticular proteins. An analysis of motifs may contribute to understanding how proteins contribute to the physical properties of cuticle as well as to the precise nature of their interaction with chitin. | genome, cuticle, cuticle protein, cuticular protein, cdna, protein, insect, exoskeleton, annotation, chitin, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
University of Athens; Athens; Greece ; NIAID AI055624 |
PMID:15453918 | biotools:cuticledb, nif-0000-02708 | https://bio.tools/cuticledb | SCR_007045 | CuticleDB - A relational database of Arthropod cuticular proteins | 2026-08-04 09:41:44 | 12 | |||||
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Atlas of Genetics and Cytogenetics in Oncology and Haematology Resource Report Resource Website 10+ mentions |
Atlas of Genetics and Cytogenetics in Oncology and Haematology (RRID:SCR_007199) | atlas, database, data or information resource | Online journal and database devoted to genes, cytogenetics, and clinical entities in cancer, and cancer-prone diseases. Its aim is to cover the entire field under study and it presents concise and updated reviews (cards) or longer texts (deep insights) concerning topics in cancer research and genomics. | gene, cytogenetic, cancer, cancer research, genomic, online journal, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools |
PMID:23161685 | Freely available, Available to the scientific community | nif-0000-30129, biotools:atlasgeneticsoncology | https://bio.tools/atlasgeneticsoncology | SCR_007199 | Genetics and Cytogenetics Atlas | 2026-08-04 09:41:46 | 38 | ||||||
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DisProt - Database of Protein Disorder Resource Report Resource Website 100+ mentions |
DisProt - Database of Protein Disorder (RRID:SCR_007097) | database, data or information resource | The Database of Protein Disorder (DisProt) is a curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part. Users can BLAST sequences, browse by protein name, or view by protein function and functional subclass. | protein, protein structure, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Temple University; Pennsylvania; USA |
nif-0000-02754, r3d100010561, biotools:disprot | https://bio.tools/disprot, https://doi.org/10.17616/R3NG75 | http://divac.ist.temple.edu/disprot | SCR_007097 | DisProt | 2026-08-04 09:41:45 | 204 |
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