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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PS-Plant Framework Resource Report Resource Website 1+ mentions |
PS-Plant Framework (RRID:SCR_017032) | PS-Plant | software application, workflow software, data analysis software, 3d time-series analysis software, data or information resource, code testing framework, software resource, data processing software, time-series analysis software, data visualization software, 2d spatial image, software development tool, segmentation software, 3d visualization software, image, image analysis software | 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 | 2026-07-28 09:44:30 | 1 | ||||||
|
Gigwa Resource Report Resource Website 1+ mentions |
Gigwa (RRID:SCR_017080) | software application, service resource, data distribution software, biomaterial analysis service, data analysis software, application programming interface, data access protocol, software resource, data management software, data processing software, production service resource, web service, material analysis service, analysis service resource | 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 | 2026-07-28 09:44:30 | 2 | |||||
|
CATALYST Resource Report Resource Website 100+ mentions |
CATALYST (RRID:SCR_017127) | software application, data analysis software, software resource, data processing software, 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 | 2026-07-28 09:44:29 | 223 | |||||
|
SwiftOrtho Resource Report Resource Website 1+ mentions |
SwiftOrtho (RRID:SCR_017122) | software application, software resource, data analysis software, data processing 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 | 2026-07-28 09:44:31 | 4 | |||||||
|
ClustVis Resource Report Resource Website 500+ mentions Issue |
ClustVis (RRID:SCR_017133) | service resource, data analysis service, data access protocol, software resource, production service resource, web service, analysis 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 | 2026-07-28 09:44:31 | 798 | |||||||
|
SeQuiLa Resource Report Resource Website 1+ mentions |
SeQuiLa (RRID:SCR_017220) | software application, software resource, data analysis software, data processing software | Software tool for genomic intervals querying and processing built on top of Apache Spark. Elastic, fast and scalable SQL oriented solution for processing and querying genomic intervals. | genomic, intervals, querying, processing, Apache, Spark, SQL, analysis, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Warsaw University of Technology; Warsaw; Poland |
National Science Center ; Polish budget funds for science |
PMID:30428005 | Free, Available for download, Freely available | biotools:SeQuiLa-cov | http://biodatageeks.org/sequila/, https://bio.tools/SeQuiLa-cov | SCR_017220 | 2026-07-28 09:44:28 | 1 | ||||||
|
Comparative Metatranscriptomics Workflow Resource Report Resource Website 1+ mentions |
Comparative Metatranscriptomics Workflow (RRID:SCR_017109) | CoMW | software application, narrative resource, data analysis software, data or information resource, sequence analysis software, data processing software, software resource, workflow, training material | 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 | 2026-07-28 09:44:29 | 3 | ||||||
|
VETA Resource Report Resource Website 1+ mentions |
VETA (RRID:SCR_017201) | software application, data analysis software, software resource, data processing software, data visualization software, data acquisition software | Software suite of functions for EMG data visualization and processing. Open source Matlab toolbox for electromyography combined with transcranial magnetic stimulation. MATLAB toolbox for the collection, analysis, and visualization of EMG and TMS. | Electromyography, transcranial, magnetic, stimulation, analysis, EMG, TMS, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
NCATS TR002370 | PMID:31572120 | Free, Available for download, Freely available | BioTools:VETA, biotools:VEtA | https://github.com/greenhouselab/Veta/tree/master/data, https://bio.tools/VETA, https://bio.tools/VETA, https://bio.tools/VETA | SCR_017201 | 2026-07-28 09:44:31 | 2 | ||||||
|
HaTSPiL Resource Report Resource Website 1+ mentions |
HaTSPiL (RRID:SCR_017059) | software application, data analysis software, sequence analysis software, software resource, data processing software | 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 | 2026-07-28 09:44:28 | 1 | ||||||||
|
PRSice Resource Report Resource Website 50+ mentions |
PRSice (RRID:SCR_017057) | software application, software resource, data analysis software, data processing 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 | 2026-07-28 09:44:26 | 97 | |||||
|
CentroidFold Resource Report Resource Website 10+ mentions |
CentroidFold (RRID:SCR_017253) | software application, data access protocol, software resource, web service, simulation software | Web server for RNA secondary structure prediction. Predicts RNA secondary structure from RNA sequence. Based on generalized centroid estimator. | RNA, secondary, structure, prediction, centroid, estimator, sequecne, data, alignment, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
New Energy and Industrial Technology Development Organization of Japan ; Ministry of Education ; Culture ; Sports ; Science and Technology of Japan ; Internal fund of Computational Biology Research Center |
PMID:19435882 | Free, Freely available | biotools:centroidfold, OMICS_03449 | https://bio.tools/centroidfold | SCR_017253 | 2026-07-28 09:44:28 | 15 | ||||||
|
ape Resource Report Resource Website 10+ mentions |
ape (RRID:SCR_017343) | software application, software resource, data analysis software, data processing software | Software R package for analysis of phylogenetics and evolution. Environment for modern phylogenetics and evolutionary analyses in R. | analysis, phylogenetics, evolution, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: CRAN |
PMID:30016406 PMID:14734327 PMID:22495750 |
Free, Available for download, Freely available | biotools:ape | https://cran.r-project.org/web/packages/ape/ape.pdf, http://ape-package.ird.fr/, https://bio.tools/ape | SCR_017343 | ape 3.0, ape 5.0, Analysis of Phylogenetics and Evolution | 2026-07-28 09:44:33 | 42 | ||||||
|
prank Resource Report Resource Website 100+ mentions |
prank (RRID:SCR_017228) | software application, software toolkit, software resource, data processing software, alignment software, image analysis software | Software application as probabilistic multiple alignment program for DNA, codon and amino-acid sequences. Allows for defining potential structure for sequences to be aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences. | multiple, nucleotide, sequence, alignment, DNA, codon, amino acid, phylogenetic, gap, predict, location, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Helsinki; Helsinki; Finland |
PMID:24170401 PMID:21110866 |
Free, Available for download, Freely available | biotools:prank, SCR_024174, OMICS_12425 | https://www.ebi.ac.uk/goldman-srv/webprank/, https://ariloytynoja.github.io/prank-msa/, https://bio.tools/prank | https://omictools.com/prank-tool | SCR_017228 | PRANK | 2026-07-28 09:44:32 | 253 | |||||
|
miRpathDB Resource Report Resource Website 50+ mentions |
miRpathDB (RRID:SCR_017356) | data or information resource, database, data access protocol, software resource, web service | Collection of single miRNAs that regulate pathways, gene ontologies and other categories, hence complementing available miRNA target enrichment programs, tailored for miRNA sets. New dictionary on microRNAs and target pathways. Database to augment available target pathway web-servers by providing researches access to information which pathways are regulated by miRNA, which miRNAs target pathway and how specific regulations are. | Collection, miRNA, data, pathway, gene, ontology, dataset, dictionary, target, regulation, bio.tools |
is listed by: bio.tools is listed by: Debian |
Saarland University ; Germany |
PMID:27742822 | biotools:miRPathDb | https://bio.tools/miRPathDB | SCR_017356 | miRNA Pathway Dictionary Database | 2026-07-28 09:44:29 | 52 | ||||||
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GraphClust2 Resource Report Resource Website 1+ mentions |
GraphClust2 (RRID:SCR_017286) | software application, web application, data analysis software, software resource, data processing software | Software tool for scalable clustering of RNAs based on sequence and secondary structures similarities. Implemented within Galaxy framework. Used for studying RNA function. | scalable, clustering, RNA, sequence, secondary, structure, function, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Freiburg; Baden-Wurttemberg; Germany |
German Research Foundation Collaborative Research Centre 992 Medical Epigenetics ; German Federal Ministry of Education and Research |
PMID:31808801 PMID:22689765 |
Free, Available for download, Freely available | biotools:GraphClust2 | https://bio.tools/GraphClust2 | SCR_017286 | GraphClust, GraphClust-2 | 2026-07-28 09:44:33 | 4 | |||||
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Proovread Resource Report Resource Website 10+ mentions |
Proovread (RRID:SCR_017331) | software application, data analysis software, sequence analysis software, software resource, data processing software | Software tool for PacBio hybrid error correction through iterative short read consensus. | PacBio, hybrid, error, correction, short, read, consensus, DNA, sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: BWA is related to: BLASR is related to: SHRiMP |
European Research Council | PMID:25015988 | Free, Available for download, Freely available | biotools:proovread | https://bio.tools/proovread | SCR_017331 | 2026-07-28 09:44:29 | 12 | ||||||
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European Variation Archive (EVA) Resource Report Resource Website 50+ mentions |
European Variation Archive (EVA) (RRID:SCR_017425) | EVA | service resource, data or information resource, data repository, database, storage service resource | Open access database of all types of genetic variation data from all species. Users can download data from any study, or submit their own data to archive. You can also query all variants by study, gene, chromosomal location or dbSNP identifier using our Variant Browser. | Collection, genetic, variation, data, chromosomal, location, dbSNP, 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: bio.tools is listed by: Debian |
Free, Freely available | biotools:eva | https://bio.tools/eva | SCR_017425 | EVA, European Variation Archive | 2026-07-28 09:44:35 | 89 | ||||||
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Galaxy scater Resource Report Resource Website 1+ mentions |
Galaxy scater (RRID:SCR_017394) | software application, service resource, data analysis software, sequence analysis software, source code, software resource, data processing software, software toolkit, training service resource | Software tool as Galaxy based training resource for single cell RNA-seq quality control and analyses. | scRNA-seq, single, cell, scater, Galaxy, training, quality, control, bio.tools |
is listed by: Debian is listed by: bio.tools |
BBSRC BBS/E/T/000PR9817; BBSRC BBS/E/T/000PR9818; BBSRC BBS/E/T/000PR9819; BBSRC CCG:BBS/E/T/000PR9816 |
DOI:10.1101/724047 | Free, Available for download, Freely available | biotools:Galaxy_scater | https://bio.tools/Galaxy_scater | SCR_017394 | 2026-07-28 09:44:29 | 1 | ||||||
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Multiple Myeloma survival predictor Resource Report Resource Website 1+ mentions |
Multiple Myeloma survival predictor (RRID:SCR_017651) | service resource, software resource, data access protocol, web service | Dockerized environment for winning algorithm in 2017 Multiple Myeloma DREAM Challenge, Sub-Challenge 3. | Multiple Myeloma, prognostic model, survival analysis, GuanRank, bio.tools |
is listed by: bio.tools is listed by: Debian |
Multiple Myeloma | Restricted | biotools:Multiple_Myeloma_survival_prediction | https://bio.tools/Multiple_Myeloma_survival_prediction | SCR_017651 | 2026-07-28 09:44:36 | 2 | |||||||
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MCScan Resource Report Resource Website 10+ mentions |
MCScan (RRID:SCR_017650) | software application, data analysis software, sequence analysis software, software resource, data processing software, software toolkit | Software package to simultaneously scan multiple genomes to identify homologous chromosomal regions and subsequently align these regions using genes as anchors.Used to identify conserved gene arrays both within same genome and across different genomes. Command line program to wrap dagchainer and combine pairwise results into multi alignments in column format. | Simultaneously, scan, multiple, genome, identify, homologous, chromosomal, region, align, gene, anchor, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Georgia; Georgia; USA |
Free, Available for downoad, Freely available | biotools:MCScan | http://chibba.agtec.uga.edu/duplication/mcscan/, https://bio.tools/MCScan | SCR_017650 | Multiple Collinearity Scan | 2026-07-28 09:44:32 | 37 |
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