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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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timecourse Resource Report Resource Website 1+ mentions |
timecourse (RRID:SCR_000077) | timecourse | software resource | Software functions for data analysis and graphical displays for developmental microarray time course data. | microarray, differential expression, time course, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: CRAN has parent organization: Bioconductor has parent organization: University of California at Berkeley; Berkeley; USA |
Free, Available for download, Freely available | OMICS_01980, biotools:timecourse | https://bio.tools/timecourse | SCR_000077 | SciCrunch Registry | timecourse - Statistical Analysis for Developmental Microarray Time Course Data | 2026-10-10 12:35:28 | 5 | ||||||
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Patchwork Resource Report Resource Website 10+ mentions |
Patchwork (RRID:SCR_000072) | Patchwork | software resource | Software tool for analyzing and visualizing allele-specific copy numbers and loss-of-heterozygosity in cancer genomes. The data input is in the format of whole-genome sequencing data which enables characterization of genomic alterations ranging in size from point mutations to entire chromosomes. High quality results are obtained even if samples have low coverage, ~4x, low tumor cell content or are aneuploid. Patchwork takes BAM files as input whereas PatchworkCG takes input from CompleteGenomics files. TAPS performs the same analysis as Patchwork but for microarray data. | genome, allele, copy number, bam, unix, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Uppsala University; Uppsala; Sweden |
Cancer, Tumor | PMID:23531354 | Free, Available for download, Freely available | biotools:patchwork, OMICS_02118 | https://bio.tools/patchwork | SCR_000072 | SciCrunch Registry | 2026-10-10 12:35:28 | 10 | |||||
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SNAVI Resource Report Resource Website |
SNAVI (RRID:SCR_000091) | software resource | Desktop application for analysis and visualization of large-scale cell signaling networks. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code |
PMID:19154595 | Free, Available for download, Freely available | biotools:snavi, OMICS_04122 | https://bio.tools/snavi | SCR_000091 | SciCrunch Registry | Signaling Networks Analysis and Visualization | 2026-10-10 12:35:29 | 0 | ||||||
|
CovalentDock Cloud Resource Report Resource Website |
CovalentDock Cloud (RRID:SCR_000126) | CovalentDock Cloud | data access protocol, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Web service that is used by researchers and scientists to perform protein-ligand covalent docking. This form allows for the formation of covalent linkages between the ligand and the receptor. | protein ligand covalent docking, ligand, receptor, covalent linkage, data analysis service, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23034731 | THIS RESOURCE IS NO LONGER IN SERVICE | covalentdock_cloud, OMICS_01597 | https://bio.tools/covalentdock_cloud | SCR_000126 | SciCrunch Registry | 2026-10-10 12:35:30 | 0 | ||||||
|
Dipy Resource Report Resource Website 10+ mentions |
Dipy (RRID:SCR_000029) | DIPY | data analysis software, data processing software, software application, software resource, software toolkit | Software Python package for analyzing diffusion data. Software library for analysis of diffusion MRI data. | MRI, magnetic resonance, diffusion data analysis, diffusion MRI data, diffusion MRI data analysis, |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian has parent organization: Neuroimaging in Python has parent organization: University of Cambridge; Cambridge; United Kingdom |
PMID:24600385 | Free, Available for download, Freely available | nlx_155745 | https://sources.debian.org/src/python-dipy/, http://www.nitrc.org/projects/dipy, http://elef.soic.indiana.edu/, https://github.com/nipy/dipy_web, | http://nipy.org/dipy/ | SCR_000029 | SciCrunch Registry | Diffusion Imaging In Python, NIPY Diffusion Imaging Analysis | 2026-10-10 12:35:27 | 16 | ||||
|
Fusion Analyser Resource Report Resource Website |
Fusion Analyser (RRID:SCR_000059) | data analysis software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16, 2023. Software used to detect gene fusions from paired-end RNA-Seq data. | gene fusion, rna-seq, paired-end rna-seq data, fusion event, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:22570408 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01347, biotools:fusionanalyser | https://bio.tools/fusionanalyser | SCR_000059 | SciCrunch Registry | FusionAnalyser | 2026-10-10 12:35:28 | 0 | ||||||
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CorMut Resource Report Resource Website |
CorMut (RRID:SCR_000053) | data analysis software, data processing software, sequence analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Software package for computing correlated mutations based on selection pressure. Three methods are provided for detecting correlated mutations, including conditional selection pressure, mutual information and Jaccard index. The computation consists of two steps: First, the positive selection sites are detected; second, the mutation correlations are computed among the positive selection sites. Note that the first step is optional. Meanwhile, CorMut facilitates the comparison of the correlated mutations between two conditions by the means of correlated mutation network. | sequencing, correlated mutation, selection pressure, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: CRAN has parent organization: Bioconductor |
PMID:24681904 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_03636, biotools:cormut | https://bio.tools/cormut | SCR_000053 | SciCrunch Registry | CorMut - Detect the correlated mutations based on selection pressure | 2026-10-10 12:35:27 | 0 | ||||||
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pairheatmap Resource Report Resource Website |
pairheatmap (RRID:SCR_003109) | software resource | A software tool to compare two heatmaps and discover patterns within and across groups. In the context of biology, group can be defined based on gene ontology. | standalone software, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: CRAN |
PMID:24016862 | Free, Available for download, Freely available | biotools:pairheatmap, OMICS_04853 | https://www.rdocumentation.org/packages/pairheatmap/versions/1.0.1/topics/pairheatmap | SCR_003109 | SciCrunch Registry | pairheatmap: A tool for comparing heatmaps | 2026-10-10 12:36:32 | 0 | ||||||
|
MFEprimer Resource Report Resource Website 10+ mentions |
MFEprimer (RRID:SCR_003066) | software resource | A fast thermodynamics-based software program for checking PCR primer specificity against genomic DNA and mRNA/cDNA sequence databases. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:22689644 | Free, Available for download, Freely available | biotools:mfeprimer-2.0, OMICS_02355 | https://www.mfeprimer.com/ | SCR_003066 | SciCrunch Registry | MFEprimer-2.0 | 2026-10-10 12:36:21 | 21 | ||||||
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MIPE Resource Report Resource Website 10+ mentions |
MIPE (RRID:SCR_003065) | data or information resource, interchange format, narrative resource, software resource, standard specification | A XML format that enables genomics researchers to store critical information on PCR experiments. Accompagnying perl scripts are written to read from (dbSTS) or write to a MIPE XML file. | standalone software, pcr, xml, data storage, data exchange |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_02358 | http://mipe.sourceforge.net/, https://sources.debian.org/src/mipe/ | SCR_003065 | SciCrunch Registry | Minimal Information for PCR Experiments | 2026-10-10 12:36:46 | 32 | |||||||
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eQtlBma Resource Report Resource Website 1+ mentions |
eQtlBma (RRID:SCR_003102) | software resource | Software package that implements Bayesian statistical methods to detect eQTLs jointly in multiple subgroups (e.g. tissues). Key features are to borrow information across subgroups, to explicitly model heterogeneity (qualitatively and quantitatively), and to borrow information across genes to estimate hyper-parameters from the data (empirical Bayes). | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Chicago; Illinois; USA |
PMID:23671422 | Free, Available for download, Freely available | biotools:eqtlbma, OMICS_04875 | https://bio.tools/eqtlbma | SCR_003102 | SciCrunch Registry | 2026-10-10 12:36:46 | 6 | |||||||
|
Triplex Resource Report Resource Website 10+ mentions |
Triplex (RRID:SCR_003061) | software resource | Software package that provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many canonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D. | software package, mac os x, unix/linux, windows, r, gene regulation, sequence matching, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23709494 | Free, Available for download, Freely available | OMICS_06259, biotools:triplex | http://www.fi.muni.cz/~lexa/triplex/, https://bio.tools/triplex | SCR_003061 | SciCrunch Registry | triplex - Search and visualize intramolecular triplex-forming sequences in DNA | 2026-10-10 12:36:21 | 10 | ||||||
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mrsFAST Resource Report Resource Website 10+ mentions |
mrsFAST (RRID:SCR_003128) | mrsFAST | software resource | A cache-oblivious algorithm designed to map short reads to reference genome assemblies in a fast and memory-efficient manner. It optimizes cache usage to get higher performance. Currently Supported Features: * Mistmatches, No indels * Paired-end Mapping Mode * Discordant Paired-end Mapping Mode (to be used in conjuction with Variation Hunter) | next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SPLITREAD has parent organization: SourceForge |
PMID:20676076 | Free, Available for download, Freely available | biotools:mrsfast, nlx_156780 | https://bio.tools/mrsfast | SCR_003128 | SciCrunch Registry | mrsFAST: micro-read substitution-only Fast Alignment Search Tool, micro-read substitution-only Fast Alignment Search Tool | 2026-10-10 12:36:23 | 22 | |||||
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HYDEN Resource Report Resource Website 10+ mentions |
HYDEN (RRID:SCR_003126) | HYDEN | software resource | Software program for designing pairs of degenerate primers for a given set of DNA sequences. It works well for large input sets of genomic sequences (e.g., hundreds of sequences of length 1Kbp). It is a batch (i.e., command-line, as opposed to graphical interface) program, available for Windows XP (downloadable version) and Linux (upon request). | degenerate, primer, dna sequence, primer design, degenerate primer, windows, linux, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Tel Aviv University; Ramat Aviv; Israel |
PMID:17951798 | Free, Available for download, Freely available | OMICS_02338, biotools:hyden | https://bio.tools/hyden | SCR_003126 | SciCrunch Registry | HYDEN - A Software for Designing Degenerate Primers, HighlY DEgeNerate primers | 2026-10-10 12:36:47 | 12 | |||||
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Eukaryotic Linear Motif Resource Report Resource Website 100+ mentions |
Eukaryotic Linear Motif (RRID:SCR_003085) | ELM | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Computational biology resource for investigating candidate functional sites in eukarytic proteins. Functional sites which fit to the description linear motif are currently specified as patterns using Regular Expression rules. To improve the predictive power, context-based rules and logical filters are being developed and applied to reduce the amount of false positives. The current version of the ELM server provides core functionality including filtering by cell compartment, phylogeny, globular domain clash (using the SMART/Pfam databases) and structure. In addition, both the known ELM instances and any positionally conserved matches in sequences similar to ELM instance sequences are identified and displayed (see ELM instance mapper). Although the ELM resource contains a large collection of functional site motifs, the current set of motifs is not exhaustive. | linear motif, regulatory protein, motif, protein sequence, functional site, prediction, disease, virus, cell compartment, phylogeny, globular domain clash, structure, protein, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: SMART is related to: Pfam has parent organization: European Molecular Biology Laboratory |
EMBL international PhD program ; EMBL Interdisciplinary PostDoc fellowship ; Federal Government Department of Education and Science FKZ01GS0862; European Community Seventh Framework Programme FP7/2009 241955; European Community Seventh Framework Programme FP7/2009 242129; Polish Ministry of Science and Higher Education IP2010-0483-70; Biotechnology and Biological Sciences Research Council BB/F010486/1; Region Alsace and College Doctoral Europeen ; Science Foundation Ireland 08/IN.1/B1864; BBSRC BB/I006230/1; German Research Foundation SFB796; Swiss National Science Foundation |
PMID:22110040 | Free, Available for download, Freely available | biotools:elm, nif-0000-30486 | https://bio.tools/elm | SCR_003085 | SciCrunch Registry | Eukarotic Linear Motif resource for Functional Sites in Proteins | 2026-10-10 12:36:22 | 325 | ||||
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BioJS Resource Report Resource Website 10+ mentions |
BioJS (RRID:SCR_003119) | BioJS | data processing software, data visualization software, software application, software library, software resource, software toolkit | An open source JavaScript library of components for visualisation of biological data on the web. | javascript, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: The Genome Analysis Centre; Norwich; United Kingdom has parent organization: European Bioinformatics Institute |
BBSRC ; NHLBI HHSN268201000035C; European Union PSIMEx FP7-HEALTH-2007-223411 |
PMID:23435069 | Free, Freely available | biotools:biojs, nlx_156742 | http://www.ebi.ac.uk/Tools/biojs/registry/, https://bio.tools/biojs | http://www.tgac.ac.uk/tools-resources/biojs/ | SCR_003119 | SciCrunch Registry | 2026-10-10 12:36:33 | 22 | ||||
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bwtool Resource Report Resource Website 10+ mentions |
bwtool (RRID:SCR_003035) | software resource | A command-line utility for bigWig files designed to read bigWig files rapidly and efficiently, providing functionality for extracting data and summarizing it in several ways, globally or at specific regions. Its functionality is subdivided into subprograms that roughly fall into three categories: data extraction, analysis, and data modification, although e.g. in the case of the matrix program or the sax program, the boundary between data extraction and analysis isn't very strong. The data modification programs all have the behavior that a bigWig is inputted and a new bigWig is outputted. | standalone software, unix/linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:2448936 | Free, Available for download, Freely available | biotools:bwtool, OMICS_05125 | https://bio.tools/bwtool | SCR_003035 | SciCrunch Registry | 2026-10-10 12:36:20 | 22 | |||||||
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Cytoscape Resource Report Resource Website 10000+ mentions |
Cytoscape (RRID:SCR_003032) | data analysis software, data processing software, data visualization software, software application, software resource | Software platform for complex network analysis and visualization. Used for visualization of molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. | biological, network, visualization, analysis, data, gene, pathway, molecular, interaction, FASEB list |
is used by: CytoSPADE is used by: HDBase is used by: DisGeNET is used by: categoryCompare lists: PEPPER is listed by: Debian is listed by: SoftCite is related to: PhosphoSitePlus: Protein Modification Site is related to: TRIP Database is related to: CoryneRegNet is related to: AltAnalyze - Alternative Splicing Analysis Tool is related to: MiMI Plugin for Cytoscape is related to: Network Data Exchange (NDEx) is related to: GeneMANIA is related to: DroID - Drosophila Interactions Database is related to: Network-based Prediction of Human Tissue-specific Metabolism is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: DaTo is related to: PiNGO is related to: iBIOFind is related to: cPath is related to: BiNGO: A Biological Networks Gene Ontology tool is related to: ClueGO is related to: RamiGO is related to: EGAN: Exploratory Gene Association Networks has parent organization: Institute for Systems Biology; Washington; USA has parent organization: University of California at San Diego; California; USA is parent organization of: JEPETTO has plug in: CluePedia Cytoscape plugin has plug in: CytoSPADE has plug in: EnrichmentMap has plug in: cytoHubba has plug in: iRegulon works with: NetCirChro works with: IMEx - The International Molecular Exchange Consortium works with: yFiles Layout Algorithms works with: RCy3 |
National Resource for Network Biology ; NCRR RR031228; NIGMS GM070743 |
PMID:21149340 PMID:14597658 |
Free, Available for download, Freely available | nif-0000-30404 | https://sources.debian.org/src/cytoscape/ | SCR_003032 | SciCrunch Registry | Complex Network Analysis Visualization, Cytoscape 2.6, Cytoscape 3.0 | 2026-10-10 12:36:30 | 25317 | |||||
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SMRT View Resource Report Resource Website 1+ mentions |
SMRT View (RRID:SCR_003029) | software resource | An open source Genome Browser that visualizes data generated by PacBio Sequencing Systems. * Users can explore and interact with all types of analysis results, including resequencing, De novo, cDNA, and barcoding. * Users can also visualize base modifications, base identification and motifs analysis results. | standalone software, unix/linux, mac os x, windows, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:smrt_view, OMICS_05137 | https://bio.tools/smrt_view | SCR_003029 | SciCrunch Registry | SMRT-View | 2026-10-10 12:36:20 | 9 | |||||||
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ISFinder Resource Report Resource Website 1000+ mentions |
ISFinder (RRID:SCR_003020) | ISFinder | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | Database of a list of insertion sequences isolated from eubacteria and archaea. It is organized into individual files containing their general features (name, size, origin, family.....) as well as their DNA and potential protein sequences. Although most of the entries have been identified as individual elements, a growing number are included from their description in sequenced bacterial genomes. The search engine permits the retrieval and display of individual and groups of ISs based on a combination of their general features. Two levels of search are available. The simple search option enables the user to sort elements using a limited number of basic items whereas the extensive search offers an additional set of possibilities such as comparisons of the sequences of terminal inverted repeats and a variety of different layout displays. Built in links are provided to: the EMBL sequence database, the NCBI taxonomy database and to the ESF plasmid database. At present, only individual sequences can be downloaded one by one for comparison. An on-line BLAST facility is available and in future versions direct access to additional analytical tools will be provided on line. Direct submission of ISs is encouraged using the on-line form provided. | insertion sequence, insertion, sequence, blast, dna, protein sequence, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Paul Sabatier University - Toulouse III; Toulouse; France |
CNRS | PMID:22367867 PMID:19906702 |
biotools:isfinder, nif-0000-03050 | https://bio.tools/isfinder | SCR_003020 | SciCrunch Registry | IS Finder, Isfinder | 2026-10-10 12:36:30 | 1181 |
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