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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Flye Resource Report Resource Website 100+ mentions |
Flye (RRID:SCR_017016) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software package as de novo assembler for single molecule sequencing reads. Used for assembling long, error prone reads such as those produced by PacBio and Oxford Nanopore Technologies, for fast and accurate genome reconstructions. Available for Linux and MacOS platforms. | assembler, single, molecule, sequencing, long, error, read, fast, accurate, genome, reconstruction, nucleotide, quality, data, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of California at San Diego; California; USA |
PMID:27956617 | Free, Available for download, Freely available | biotools:Flye | https://bio.tools/Flye, https://sources.debian.org/src/flye/ | SCR_017016 | 2026-09-12 12:58:47 | 324 | |||||||
|
Experimental Design Assistant Resource Report Resource Website 100+ mentions |
Experimental Design Assistant (RRID:SCR_017019) | EDA | service resource, software resource, web application | 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 | 2026-09-12 12:58:47 | 192 | |||||
|
Comparative Metatranscriptomics Workflow Resource Report Resource Website 1+ mentions |
Comparative Metatranscriptomics Workflow (RRID:SCR_017109) | CoMW | data analysis software, data or information resource, data processing software, narrative resource, sequence analysis software, software application, software resource, training material, workflow | 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 | 2026-09-12 12:58:48 | 3 | ||||||
|
HaTSPiL Resource Report Resource Website 1+ mentions |
HaTSPiL (RRID:SCR_017059) | data analysis software, data processing software, sequence analysis software, software application, software resource | 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 | 2026-09-12 12:58:47 | 1 | ||||||||
|
PRSice Resource Report Resource Website 100+ mentions |
PRSice (RRID:SCR_017057) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-12 12:58:47 | 110 | |||||
|
Heatmapper Resource Report Resource Website 100+ mentions |
Heatmapper (RRID:SCR_016974) | data access protocol, data processing software, software application, software resource, web service | 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 | 2026-09-12 12:58:46 | 252 | |||||
|
BinPacker Resource Report Resource Website 10+ mentions |
BinPacker (RRID:SCR_017038) | data analysis software, data processing software, software application, software resource | 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 ; NCRR P20 RR01 6460; NIGMS P20 GM103429; NSF 1553680 |
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 | 2026-09-12 12:58:47 | 10 | ||||||
|
PS-Plant Framework Resource Report Resource Website 1+ mentions |
PS-Plant Framework (RRID:SCR_017032) | PS-Plant | 2d spatial image, 3d time-series analysis software, 3d visualization software, code testing framework, data analysis software, data or information resource, data processing software, data visualization software, image, image analysis software, segmentation software, software application, software development tool, software resource, time-series analysis software, workflow 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/M025551/1; BBSRC BB/N005147/1; BBSRC BB/N02334X/1 |
Free, Available for download, Freely available | biotools:PS-Plant | https://bio.tools/PS-Plant | SCR_017032 | 2026-09-12 12:58:47 | 1 | ||||||
|
ClustVis Resource Report Resource Website 500+ mentions Issue |
ClustVis (RRID:SCR_017133) | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | 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 |
EFPIA ; Estonian Research Council ; European Commission ; European Federation of Pharmaceutical Industries and Associations ; European Regional Development Fund ; European Union Seventh Framework Programme ; Innovative Medicines Initiative Joint Undertaking |
PMID:25969447 | biotools:clustvis, OMICS_08539 | https://github.com/taunometsalu/ClustVis, https://bio.tools/clustvis | SCR_017133 | 2026-09-12 12:58:49 | 974 | |||||||
|
CentroidFold Resource Report Resource Website 10+ mentions |
CentroidFold (RRID:SCR_017253) | data access protocol, simulation software, software application, software resource, web service | 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 |
Internal fund of Computational Biology Research Center ; Ministry of Education ; Culture ; Sports ; Science and Technology of Japan ; New Energy and Industrial Technology Development Organization of Japan |
PMID:19435882 | Free, Freely available | biotools:centroidfold, OMICS_03449 | https://bio.tools/centroidfold | SCR_017253 | 2026-09-12 12:58:50 | 17 | ||||||
|
WTDBG Resource Report Resource Website 50+ mentions |
WTDBG (RRID:SCR_017225) | alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource | Software tool as de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies. It assembles raw reads without error correction and then builds consensus from intermediate assembly output. Desiged to assemble huge genomes in very limited time. | sequence, assembler, de novo, long, noisy, read, likelihood, estimator, genome |
is listed by: OMICtools is listed by: Debian |
NHGRI R01 HG010040; NSFC |
PMID:31819265 | Free, Available for download, Freely available | OMICS_24025 | https://github.com/ruanjue/wtdbg, https://sources.debian.org/src/wtdbg2/ | SCR_017225 | Wtdbg2, wtdgb, Wtdgb, wtdgb2 | 2026-09-12 12:58:50 | 66 | |||||
|
prank Resource Report Resource Website 100+ mentions |
prank (RRID:SCR_017228) | alignment software, data processing software, image analysis software, software application, software resource, software toolkit | 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 | 2026-09-12 12:58:50 | 281 | |||||
|
SeQuiLa Resource Report Resource Website 1+ mentions |
SeQuiLa (RRID:SCR_017220) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-12 12:58:50 | 1 | ||||||
|
VETA Resource Report Resource Website 1+ mentions |
VETA (RRID:SCR_017201) | data acquisition software, data analysis software, data processing software, data visualization software, software application, software resource | 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 | 2026-09-12 12:58:49 | 2 | ||||||
|
ape Resource Report Resource Website 50+ mentions |
ape (RRID:SCR_017343) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-12 12:58:51 | 52 | ||||||
|
miRpathDB Resource Report Resource Website 50+ mentions |
miRpathDB (RRID:SCR_017356) | data access protocol, data or information resource, database, 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 | 2026-09-12 12:58:52 | 73 | ||||||
|
GraphClust2 Resource Report Resource Website 1+ mentions |
GraphClust2 (RRID:SCR_017286) | data analysis software, data processing software, software application, software resource, web application | 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 Federal Ministry of Education and Research ; German Research Foundation Collaborative Research Centre 992 Medical Epigenetics |
PMID:31808801 PMID:22689765 |
Free, Available for download, Freely available | biotools:GraphClust2 | https://bio.tools/GraphClust2 | SCR_017286 | GraphClust, GraphClust-2 | 2026-09-12 12:58:51 | 4 | |||||
|
Proovread Resource Report Resource Website 10+ mentions |
Proovread (RRID:SCR_017331) | data analysis software, data processing software, sequence analysis software, software application, software resource | 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 | 2026-09-12 12:58:51 | 14 | ||||||
|
Phangorn Resource Report Resource Website 10+ mentions |
Phangorn (RRID:SCR_017302) | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | Software R package for phylogenetic reconstruction and analysis. Used for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation. Allows to compare trees, models selection and offers visualizations for trees and split networks. | phylogenetic, tree, network, reconstruction, analysis, estimation, Maximum, Likelihood, Parsimony, distance, method, Hadamard conjugation |
is listed by: Debian is listed by: OMICtools is related to: CRAN |
Muséum National D Histoire Naturelle | DOI:10.1093/bioinformatics/btq706 | Free, Available for download, Freely available | OMICS_12497 | https://github.com/KlausVigo/phangorn, https://sources.debian.org/src/r-cran-phangorn/ | SCR_017302 | Phangorn R package | 2026-09-12 12:58:51 | 28 | |||||
|
European Variation Archive (EVA) Resource Report Resource Website 100+ mentions |
European Variation Archive (EVA) (RRID:SCR_017425) | EVA | data or information resource, data repository, database, service resource, 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 | 2026-09-12 12:58:52 | 107 |
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