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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NAT/NCS2 Hound Resource Report Resource Website 1+ mentions |
NAT/NCS2 Hound (RRID:SCR_016473) | NAT, NCS2 | data analysis software, data processing software, sequence analysis software, software application, software resource, web application | Web server for the detection and evolutionary classification of prokaryotic and eukaryotic nucleobase-cation symporters of the NAT/NCS2 family. Used to scan, identify and evolutionary classify NAT/NCS2 nucleobase transporter proteins. | protein, sequence, scan, identify, evolutionary, classify, prokaryotic, nucleobase, transporter, protein, amino acid, conserved |
is listed by: OMICtools has parent organization: University of Thessaly; Thessaly; Greece |
DOI:10.1101/332452 | Free, Available to download, Freely available | SCR_016473 | SciCrunch Registry | Nucleobase Ascorbate Transporter, NCS2:Nucleobase Cation Symporter 2 | 2026-09-26 02:15:47 | 1 | |||||||
|
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 | SciCrunch Registry | Nuclear Magnetic Resonance PROcessing FLOW, Nuclear Magnetic Resonance Processing Flow | 2026-09-26 02:15:49 | 29 | |||||
|
MutaGene Resource Report Resource Website 10+ mentions |
MutaGene (RRID:SCR_016574) | data analysis software, data processing software, software application, software resource | Software tool to explore and analyze mutagenic factors leading to tumors to decipher cancer genetic heterogeneity. | analyze, mutagenic, factor, turmor, decipher, cancer, genetic, heterogeneity | is listed by: OMICtools | National Library of Medicine ; NIH |
PMID:28472504 | Free, Available for download, Freely available | https://ncbiinsights.ncbi.nlm.nih.gov/tag/mutagene/ | SCR_016574 | SciCrunch Registry | 2026-09-26 02:15:49 | 10 | |||||||
|
NeuroAnatomy Toolbox Resource Report Resource Website 1+ mentions |
NeuroAnatomy Toolbox (RRID:SCR_016716) | nat, NAT | data analysis software, data processing software, data visualization software, image analysis software, software application, software resource | Software R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons in the context of 3D brain structures. | biological, image, data, visualization, analysis, tracing, single, neuron, 3D, structure, brain |
is listed by: OMICtools is listed by: CRAN is related to: R Project for Statistical Computing is related to: elmr has parent organization: University of Cambridge; Cambridge; United Kingdom |
DOI:10.5281/zenodo.10171 | Free, Available for download, Freely available | https://cran.r-project.org/web/packages/nat/index.html, | SCR_016716 | SciCrunch Registry | NeuroAnatomy Toolbox, neuroanatomy toolbox, Neuro Anatomy Toolbox, neuro anatomy toolbox | 2026-09-26 02:15:50 | 5 | ||||||
|
VoxBlast Resource Report Resource Website 1+ mentions |
VoxBlast (RRID:SCR_016491) | 3d visualization software, data processing software, data visualization software, image processing software, software application, software resource | Software application for science and medicine which offers 3-D Measurement, 3-D Volume Visualization, and 3-D Rendering for any 3-D data. It accepts stacks of registered 2-D images and creates 3-D projections from any viewpoint. | VayTek Inc., 3D, image, data, visualisation, reconstruction, measurement, projection, science, medicine |
is listed by: OMICtools has parent organization: University of Iowa Labs and Facilities |
Commercially available, Free demo version available | SCR_016491 | SciCrunch Registry | 2026-09-26 02:15:47 | 1 | ||||||||||
|
RNA22 Resource Report Resource Website 100+ mentions |
RNA22 (RRID:SCR_016507) | RNA22 | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool as a pattern based algorithm for detecting microRNA binding sites and their corresponding microRNA and mRNA complexes. Allows interactive exploration and visualization of miRNA target predictions. Permits link-out to external expression repositories and databases. | pattern, based, detecting, microRNA, binding, site, complex, sequence, genome, analysis, FASEB list | is listed by: OMICtools | A Star ; Singapore ; NIDDK DK04763; NIH AI54973 |
Free, Available for download, Freely available | SCR_016507 | SciCrunch Registry | RiboNucleic Acid 22 | 2026-09-26 02:15:48 | 222 | |||||||
|
miRmap Resource Report Resource Website 100+ mentions |
miRmap (RRID:SCR_016508) | data analytics software, software application, software library, software resource, software toolkit | Software application as an open source Pyton library to search and predict miRNA targets. | search, predict, miRNA, target | is listed by: OMICtools | Swiss Institute of Bioinformatics ; Swiss National Science Foundation |
PMID:23034802 | Free, Available for download, Freely available, Tutorial available | http://cegg.unige.ch/mirmap | SCR_016508 | SciCrunch Registry | 2026-09-26 02:15:48 | 227 | |||||||
|
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 | SciCrunch Registry | 2026-09-26 02:15:55 | 4 | |||||||
|
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 | SciCrunch Registry | EMAN1, EMAN2 | 2026-09-26 02:15:51 | 107 | |||
|
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 | SciCrunch Registry | prsice, PRSice-2, Polygenic Risk Score software, PRSice1, PRSice2 | 2026-09-26 02:15:54 | 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 | SciCrunch Registry | Heatmapper, HeatMapper, heat mapper | 2026-09-26 02:15:53 | 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 | SciCrunch Registry | 2026-09-26 02:15:54 | 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 | SciCrunch Registry | MITE Tracker, Miniature Inverted repeats Transposable Elements Tracker | 2026-09-26 02:15:53 | 4 | |||||
|
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 | SciCrunch Registry | 2026-09-26 02:15:57 | 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 | SciCrunch Registry | Phangorn R package | 2026-09-26 02:15:57 | 28 | |||||
|
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 | SciCrunch Registry | 2026-09-26 02:15:55 | 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 | SciCrunch Registry | 2026-09-26 02:15:56 | 17 | ||||||
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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 | SciCrunch Registry | Wtdbg2, wtdgb, Wtdgb, wtdgb2 | 2026-09-26 02:15:56 | 66 | |||||
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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 | SciCrunch Registry | PRANK | 2026-09-26 02:15:56 | 281 | |||||
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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 | SciCrunch Registry | CSBB-v3.0, CSBB-v1.0, CSBB-v2.0, Computational Suite for Bioinformaticians and Biologists | 2026-09-26 02:15:58 | 6 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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