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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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XYalign Resource Report Resource Website 1+ mentions |
XYalign (RRID:SCR_016661) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for identifying, understanding, and correcting technical biases on the sex chromosomes in next generation sequencing data. | correct, technical, bias, sex, chromosome, next, generation, sequencing, data | is listed by: OMICtools | NIGMS R35 GM124827 | DOI:10.1101/346940 | Free, Available for download, Freely available | SCR_016661 | 2026-09-19 12:53:27 | 1 | ||||||||
|
Centrifuge Classifier Resource Report Resource Website 10+ mentions |
Centrifuge Classifier (RRID:SCR_016665) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for rapid and sensitive classification of metagenomic sequences. Used for the classification of DNA sequences from microbial samples and analysis of large metagenomics data sets on conventional desktop computers. | classification, large, metagenomic, sequence, DNA, microbial, sample, analysis, data, desktop, computer, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is related to: Pavian has parent organization: Center for Computational Biology at JHU |
NHGRI R01 HG006677; NIGMS R01 GM083873; NSF ABI1356078; U. S. Army Research Office W911NF1410490 |
DOI:10.1101/gr.210641.116 | Free, Available for download, Freely available | biotools:centrifuge, OMICS_12217 | https://github.com/infphilo/centrifuge, https://bio.tools/centrifuge, https://sources.debian.org/src/centrifuge/ | SCR_016665 | 2026-09-19 12:53:27 | 10 | ||||||
|
NMRProcFlow Resource Report Resource Website 10+ mentions |
NMRProcFlow (RRID:SCR_016592) | data processing software, data visualization software, software application, software resource | Software as graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics. | NMR, metabolomics, data, viewer, spectra, processing, graphical, interface, bio.tools |
uses: R Project for Statistical Computing is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
French National Infrastructure in Metabolomics and Fluxomics | DOI:10.1007/s11306-017-1178-y | Free, Available for download, Freely available | biotools:nmrprocflow, SCR_022777 | https://github.com/INRA/NMRProcFlow, https://bio.tools/nmrprocflow, https://github.com/inra/nmrprocflow | SCR_016592 | Nuclear Magnetic Resonance PROcessing FLOW, Nuclear Magnetic Resonance Processing Flow | 2026-09-19 12:53:26 | 29 | |||||
|
EMAN Resource Report Resource Website 100+ mentions |
EMAN (RRID:SCR_016867) | EMAN | data processing software, image processing software, software application, software resource | Software suite for processing data from transmission electron microscopes. Used in supercomputing facilities as a test application for large-scale computing. Used for single particle reconstruction, helical reconstruction, 2-D crystallography and whole-cell tomography. | image, processing, data, transmission, electron, microscope, single, particle, reconstruction, helical, 2D, whole, cell, tomography, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
NIH | PMID:16859925 | Free, Available for download, Freely available | biotools:eman | https://bio.tools/eman | https://blake.bcm.edu/emanwiki/EMAN1 | SCR_016867 | EMAN1, EMAN2 | 2026-09-19 12:53:29 | 107 | |||
|
SwiftOrtho Resource Report Resource Website 1+ mentions |
SwiftOrtho (RRID:SCR_017122) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-19 12:53:34 | 4 | |||||||
|
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 | 2026-09-19 12:53:33 | 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 | 2026-09-19 12:53:31 | 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 | 2026-09-19 12:53:33 | 10 | ||||||
|
MITE-Tracker Resource Report Resource Website 1+ mentions |
MITE-Tracker (RRID:SCR_017030) | MITE Tracker | data analysis software, data processing software, sequence analysis software, software application, software resource | Open source software tool for identifying miniature inverted repeat transposable elements in large genomes. Used to process large scale genomes, to find and classify MITEs using an efficient alignment strategy to retrieve nearby inverted repeat sequences. | genomic, sequence, discover, miniature, inverted, repeat, transposable, element, clustering, cdhit |
uses: NCBI BLAST is listed by: OMICtools is related to: Python Programming Language |
National Council for Science and Technology ; Argentina ; National Institute of Agricultural Technology |
DOI:10.1186/s12859-018-2376-y | Free, Available for download, Freely available | OMICS_32242 | SCR_017030 | MITE Tracker, Miniature Inverted repeats Transposable Elements Tracker | 2026-09-19 12:53:32 | 4 | |||||
|
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 | 2026-09-19 12:53:34 | 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 | 2026-09-19 12:53:37 | 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 | 2026-09-19 12:53:36 | 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 | 2026-09-19 12:53:36 | 281 | |||||
|
Computational Suite for Bioinformaticians and Biologists Resource Report Resource Website 1+ mentions |
Computational Suite for Bioinformaticians and Biologists (RRID:SCR_017234) | CSBB | data analysis software, data processing software, software application, software resource | Software package for analysis of sequencing data. Command line based bioinformatics suite to analyze biological data acquired through biological experiments. | analysis, sequencing, data, command, line, expression, normalization, convert | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_17554 | https://github.com/csbbcompbio | SCR_017234 | CSBB-v3.0, CSBB-v1.0, CSBB-v2.0, Computational Suite for Bioinformaticians and Biologists | 2026-09-19 12:53:36 | 6 | ||||||
|
PILER Resource Report Resource Website 10+ mentions |
PILER (RRID:SCR_017333) | data analysis software, data processing software, software application, software resource | Software tool for analyzing repetitive DNA found in genome sequences. Software package for identification and classification of genomic repeats. Used for identifying patterns of local alignments induced by certain classes of repeats. | analysis, repetitive, DNA, genome, sequence, classification, alignment | is listed by: OMICtools | PMID:15961452 | Free, Available for download, Freely available | https://omictools.com/piler-tool | SCR_017333 | 2026-09-19 12:53:38 | 15 | ||||||||
|
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 | 2026-09-19 12:53:38 | 28 | |||||
|
BioAssay Express Resource Report Resource Website 1+ mentions |
BioAssay Express (RRID:SCR_017594) | data access protocol, service resource, software resource, web service | Web based tool for annotating bioassay protocols using semantic web terms. Enables searching, sorting, clustering and analyzing of assays without needing to read through original text. Exploits Common Assay Template based on underlying vocabularies and semantic standards from BioAssay Ontology, Drug Target Ontology, Cell Line Ontology and others. Users can identify similar assays and examine similarity of assays between and within organizations. | Annotating, bioassay, protocol, semantic, web, term, ontology | is listed by: OMICtools | NCATS R44 TR000185 | DOI:10.7717/peerj-cs.61 | Free, Freely available | https://github.com/cdd/bioassay-template | SCR_017594 | 2026-09-19 12:53:42 | 1 | |||||||
|
GeneATLAS Resource Report Resource Website 100+ mentions |
GeneATLAS (RRID:SCR_017577) | analysis service resource, atlas, data analysis service, data or information resource, database, production service resource, service resource | Database of associations between traits and variants using UK Biobank cohort. Searchable atlas of genetic associations. Assists researchers to query UK Biobank. Provides unbiased view of phenotype and genotype associations across of traits. | Association, trait, variant, UK Biobank, cohort, atlas, genetic, phenotype, genotype, FASEB list |
is listed by: OMICtools has parent organization: University of Edinburgh; Scotland; United Kingdom |
Free, Available for download, Freely available | SCR_017577 | Gene ATLAS, Gene Atlas | 2026-09-19 12:53:42 | 158 | |||||||||
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immuneXpresso Resource Report Resource Website |
immuneXpresso (RRID:SCR_017578) | data or information resource, service resource, software application, software resource, text-mining software | Software tool as text-mining engine that structures and standardizes knowledge of immune intercellular communication. Knowledgebase contains interactions and separate mentions of cells or cytokines in context of thousands of diseases. Intercellular interactions were text-mined from all available PubMed abstracts across disease conditions. | Structure, standardize, immune, cellular, interaction, cytokine, disease, cell, PubMed, abstract |
is listed by: NIDDK Information Network (dkNET) is listed by: OMICtools |
NIAID ; NIH ; Rappaport Family Institute for Research in the Medical Sciences |
PMID:29912209 | Free, Freely available | SCR_017578 | 2026-09-19 12:53:42 | 0 | ||||||||
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GADMA Resource Report Resource Website 1+ mentions |
GADMA (RRID:SCR_017680) | GADMA | data analysis software, data processing software, software application, software resource | Software tool to implement methods for automatic inferring joint demographic history of multiple populations from genetic data. Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data. | Inferring, demographic, history, population, genetic, data, allele, frequency, spectrum, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1101/407734 | Free, Available for download, Freely available | biotools:GADMA | https://bio.tools/GADMA | SCR_017680 | Genetic Algorithm for Demographic Model Analysis | 2026-09-19 12:53:44 | 3 |
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