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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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RStudio Resource Report Resource Website 1000+ mentions |
RStudio (RRID:SCR_000432) | RStudio | software resource | Open source and enterprise ready professional software for R statistical computing environment. Integrated development environment for R. Includes console, syntax highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. Available in open source and commercial editions and runs on desktop Windows, Mac, and Linux or in browser connected to RStudio Server or RStudio Server Pro (Debian/Ubuntu, RedHat/CentOS, and SUSE Linux). | R, statistical, computing, environment |
is used by: PlotsOfData is listed by: Debian is listed by: SoftCite is related to: rSPRITE is related to: shinyCircoss is parent organization of: Shiny is required by: circlncRNAnet |
Restricted | SciRes_000113 | https://sources.debian.org/src/rstudio/, https://posit.co/download/rstudio-desktop/ | http://www.rstudio.com/ | SCR_000432 | 2026-08-29 11:20:35 | 1191 | ||||||
|
InterProScan Resource Report Resource Website 5000+ mentions |
InterProScan (RRID:SCR_005829) | analysis service resource, data access protocol, data analysis service, data analysis software, data processing software, production service resource, service resource, software application, software resource, web service | Software package for functional analysis of sequences by classifying them into families and predicting presence of domains and sites. Scans sequences against InterPro's signatures. Characterizes nucleotide or protein function by matching it with models from several different databases. Used in large scale analysis of whole proteomes, genomes and metagenomes. Available as Web based version and standalone Perl version and SOAP Web Service. | functional, analysis, sequence, protein, nucleotide, predict, presence, domain, site, proteome, genome, metagenome, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Gene Ontology is related to: RARTF is related to: InterPro is related to: LegumeIP is related to: UniProtKB has parent organization: European Bioinformatics Institute |
Biotechnology and Biological Sciences Research Council ; EMBL ; European Union |
PMID:15980438 PMID:17202162 PMID:24451626 |
Free, Available for download, Freely available | OMICS_01479, biotools:interproscan_4, nlx_149337 | https://www.ebi.ac.uk/interpro/download.html, https://bio.tools/interproscan_4 | SCR_005829 | InterProScan Sequence Search, InterProScan 2, InterProScan 3, InterProScan 4, InterProScan 5 | 2026-08-29 11:22:25 | 7512 | |||||
|
UCSC Genome Browser Resource Report Resource Website 10000+ mentions Rating or validation data |
UCSC Genome Browser (RRID:SCR_005780) | data or information resource, database, portal, project portal, service resource | Portal to interactively visualize genomic data. Provides reference sequences and working draft assemblies for collection of genomes and access to ENCODE and Neanderthal projects. Includes collection of vertebrate and model organism assemblies and annotations, along with suite of tools for viewing, analyzing and downloading data. | Reference, sequence, assembly, collection, genome, visualize, genomic, data, ENCODE, Neanderthal, project, sequencing |
is used by: VizHub is used by: Blueprint Epigenome is used by: QmRLFS-finder is used by: International Human Epigenome Consortium Data Portal is used by: iPiG is listed by: re3data.org is listed by: OMICtools is listed by: Educational Resources in Neuroscience is listed by: SoftCite is related to: HEXEvent is related to: PicTar is related to: Phenotree is related to: Enhancer Trap Line Browser is related to: CistromeFinder is related to: ENCODE is related to: Human Epigenome Atlas is related to: ENCODE is related to: BigWig and BigBed is related to: PhenCode is related to: doRiNA is related to: ISCA Consortium is related to: WashU Epigenome Browser is related to: CRISPOR is related to: liftOver is related to: kent has parent organization: University of California at Santa Cruz; California; USA works with: TarBase works with: bedGraphToBigWig |
Alfred P. Sloan Foundation ; CISI ; David and Lucille Packard Foundation ; DOE ; HHMI ; NHGRI ; NIGMS GM52848; NIH ; NSF DBI 9809007; UC BIOTEuropean UnionH |
PMID:12045153 PMID:22908213 PMID:23155063 |
OMICS_00926, SCR_017502, nif-0000-03603, SciEx_217, SCR_012479, r3d100010243 | http://genome.cse.ucsc.edu, https://doi.org/10.17616/R3RK5C | SCR_005780 | The Human Genome Browser at UCSC, UCSC Genome Browser Group, University of California at Santa Cruz Genome Browser, UCSC Genome Bioinformatics | 2026-08-29 11:22:26 | 11041 | ||||||
|
ClueGO Resource Report Resource Website 1000+ mentions |
ClueGO (RRID:SCR_005748) | ClueGO | software resource | A Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network. It can be used in combination with GOlorize. The identifiers can be uploaded from a text file or interactively from a network of Cytoscape. The type of identifiers supported can be easily extended by the user. ClueGO performs single cluster analysis and comparison of clusters. From the ontology sources used, the terms are selected by different filter criteria. The related terms which share similar associated genes can be combined to reduce redundancy. The ClueGO network is created with kappa statistics and reflects the relationships between the terms based on the similarity of their associated genes. On the network, the node colour can be switched between functional groups and clusters distribution. ClueGO charts are underlying the specificity and the common aspects of the biological role. The significance of the terms and groups is automatically calculated. ClueGO is easy updatable with the newest files from Gene Ontology and KEGG. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | statistical analysis, function, gene ontology, pathway, annotation, network, plugin, gene |
is listed by: Gene Ontology Tools is listed by: SoftCite is related to: Gene Ontology is related to: Cytoscape is related to: KEGG is related to: BioCarta Pathways has parent organization: National Institute of Health and Medical Research; Rennes; France |
National Institute of Health and Medical Research; Rennes; France ; Ville de Paris ; INCa ; Austrian Ministry for Science and Research ; BINII ; European Union 7FP 202230 |
PMID:19237447 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149209 | SCR_005748 | 2026-08-29 11:22:29 | 2951 | ||||||
|
PHYLIP Resource Report Resource Website 1000+ mentions |
PHYLIP (RRID:SCR_006244) | PHYLIP | data processing software, software application, software resource, source code | A free package of software programs for inferring phylogenies (evolutionary trees). The source code is distributed (in C), and executables are also distributed. In particular, already-compiled executables are available for Windows (95/98/NT/2000/me/xp/Vista), Mac OS X, and Linux systems. Older executables are also available for Mac OS 8 or 9 systems. | phylogeny prediction, evolutionary tree, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite has parent organization: University of Washington; Seattle; USA works with: PAML |
NSF ; NIGMS ; DOE |
Free | nif-0000-06708, OMICS_04240, biotools:phylip | https://bio.tools/phylip, https://sources.debian.org/src/phylip/ | SCR_006244 | PHYLogeny Inference Package | 2026-08-29 11:22:34 | 3544 | |||||
|
Jalview Resource Report Resource Website 1000+ mentions |
Jalview (RRID:SCR_006459) | Jalview | software resource | A free program for multiple sequence alignment editing, visualisation and analysis that is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation. Jalview has built in DNA, RNA and protein sequence and structure visualisation and analysis capabilities. It uses Jmol to view 3D structures, and VARNA to display RNA secondary structure. | edit, analysis, annotation, multiple sequence alignment, wysiwyg, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Dundee; Scotland; United Kingdom |
BBSRC BBSB16542 | PMID:19151095 DOI:10.1093/bioinformatics/btp033 |
GNU General Public License, v3, Acknowledgement requested | OMICS_00885, biotools:Jalview | https://bio.tools/Jalview, https://sources.debian.org/src/jalview/ | SCR_006459 | 2026-08-29 11:22:37 | 4136 | |||||
|
pClamp Resource Report Resource Website 5000+ mentions |
pClamp (RRID:SCR_011323) | data acquisition software, data analysis software, data processing software, software application, software resource | Software suite for electrophysiology data acquisition and analysis by Molecular Devices. Used for the control and recording of voltage clamp, current clamp, and patch clamp experiments. The software suite consists of Clampex 11 Software for data acquisition, AxoScope 11 Software for background recording, Clampfit 11 Software for data analysis, and optional Clampfit Advanced Analysis Module for sophisticated and streamlined analysis. | electrophysiology, data, acquisition, analysis, Molecular Device, voltage, clamp, | is listed by: SoftCite | Commercially available | rid_000085 | https://www.moleculardevices.com/products/axon-patch-clamp-system/acquisition-and-analysis-software/pclamp-software-suite#gref | SCR_011323 | patch clamp, Axon™pCLAMP™ 10 Electrophysiology Data Acquisition and Analysis Software, patch CLAMP, pCLAMP 11, pCLAMP 10, patch Clamp | 2026-08-29 11:24:06 | 9999 | |||||||
|
Integrative Genomics Viewer Resource Report Resource Website 500+ mentions |
Integrative Genomics Viewer (RRID:SCR_011793) | IGV | software resource | A high-performance visualization tool for interactive exploration of large, integrated genomic datasets. | genomic datasets exploration, |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Broad Institute |
DOI:10.1038/nbt.1754 | OMICS_00917, biotools:igv | https://bio.tools/igv, https://sources.debian.org/src/igv/ | SCR_011793 | 2026-08-29 11:24:05 | 878 | |||||||
|
CANGS Resource Report Resource Website 1+ mentions |
CANGS (RRID:SCR_011837) | CANGS | data analysis software, data processing software, software application, software resource | A user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies. | windows, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
PMID:20180949 | biotools:cangs, OMICS_01084 | https://bio.tools/cangs | SCR_011837 | 2026-08-29 11:24:09 | 1 | |||||||
|
Prodigal Resource Report Resource Website 1000+ mentions |
Prodigal (RRID:SCR_011936) | Prodigal | simulation software, software application, software resource | Software tool for protein coding gene prediction for prokaryotic genomes. |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: Oak Ridge National Laboratory |
PMID:20211023 | Free, Available for download, Freely available | SCR_021246, OMICS_01493 | https://sources.debian.org/src/prodigal/ | http://prodigal.ornl.gov/ | SCR_011936 | , PROkaryotic DYnamic programming Gene-finding ALgorithm, Prokaryotic Dynamic Programming Genefinding Algorithm | 2026-08-29 11:24:13 | 3398 | |||||
|
AutoDock Resource Report Resource Website 10000+ mentions |
AutoDock (RRID:SCR_012746) | autodock | software resource | Software suite of automated docking tools. Designed to predict how small molecules, such as substrates or drug candidates, bind to receptor of known 3D structure. AutoDock consist of AutoDock 4 and AutoDock Vina. AutoDock 4 consists of autodock to perform docking of ligand to set of grids describing target protein, and autogrid to pre calculate these grids. | Small molecules receptor binding, automated docking tools, 3D structure, AutoDock 4, AutoDock Vina, ligand, docking |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Autogrid |
PMID:19399780 | Free, Available for download, Freely available | OMICS_01594, biotools:autodock | https://bio.tools/autodock, https://sources.debian.org/src/autodock/ | SCR_012746 | 2026-08-29 11:24:32 | 13612 | ||||||
|
ChIPpeakAnno Resource Report Resource Website 100+ mentions |
ChIPpeakAnno (RRID:SCR_012828) | ChIPpeakAnno | software resource | Software package that includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements. |
is listed by: OMICtools is listed by: SoftCite has parent organization: Bioconductor |
OMICS_00804 | SCR_012828 | 2026-08-29 11:24:34 | 480 | ||||||||||
|
minfi Resource Report Resource Website 100+ mentions |
minfi (RRID:SCR_012830) | minfi | data analysis software, data processing software, data visualization software, software application, software resource | Software tools for analyzing and visualizing Illumina''s 450k array data. | Illumina, array data, Analyze Illumina Infinium DNA methylation arrays, DNA methylation array, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: SWAN has parent organization: Bioconductor |
PMID:28035024 | Free, Available for download, Freely available | biotools:minfi, OMICS_00799, BioTools:minfi | https://bio.tools/minfi, https://bio.tools/minfi, https://bio.tools/minfi | SCR_012830 | 2026-08-29 11:24:22 | 417 | ||||||
|
RepeatMasker Resource Report Resource Website 10000+ mentions |
RepeatMasker (RRID:SCR_012954) | software resource | Software tool that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Currently over 56% of human genomic sequence is identified and masked by the program. Sequence comparisons in RepeatMasker are performed by one of several popular search engines including nhmmer, cross_match, ABBlast/WUBlast, RMBlast and Decypher. RepeatMasker makes use of curated libraries of repeats and currently supports Dfam ( profile HMM library ) and RepBase ( consensus sequence library ). |
uses: Repbase uses: RMBlast is listed by: Debian is listed by: OMICtools is listed by: SoftCite |
DOI:10.1007/978-1-61779-603-6_2 | nlx_156840, OMICS_09436 | https://sources.debian.org/src/repeatmasker/ | SCR_012954 | repeatmasker.org | 2026-08-29 11:24:25 | 10730 | ||||||||
|
affy Resource Report Resource Website 1000+ mentions |
affy (RRID:SCR_012835) | Affy | data analysis software, data processing software, software application, software resource | Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis. | analysis, oligonucleotide, array, Affymetrix, process, probe, data, function, bio.tools |
is listed by: OMICtools is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: affydata is related to: R Project for Statistical Computing is related to: OMICtools |
Danish Biotechnology Instrument Center | PMID:14960456 | Free, Available for download, Freely available | BioTools:affy, OMICS_00740, biotools:affy | https://bio.tools/affy, https://sources.debian.org/src/r-bioc-affy/ | SCR_012835 | Affymetrix, analysis of Affymetrix GeneChip data at the probe level, analysis of Affymetrix GeneChip data | 2026-08-29 11:24:23 | 3073 | ||||
|
TopHat Resource Report Resource Website 5000+ mentions Rating or validation data |
TopHat (RRID:SCR_013035) | alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource | Software tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions. | align, RNA-Seq, read, cDNA, sequencing, transcriptomics, fast, splice, junction, mapper, exon, analysis, bio.tools |
uses: Bowtie is used by: CIRCexplorer is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: HISAT2 has parent organization: University of Maryland; Maryland; USA has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Johns Hopkins University; Maryland; USA has parent organization: University of Washington; Seattle; USA works with: GeneScissors |
NHGRI R01 HG006102; NHGRI R01 HG006677 |
PMID:23618408 PMID:19289445 DOI:10.1093/bioinformatics/btp120 |
Free, Available for download, Freely available | biotools:tophat, OMICS_01257 | https://github.com/infphilo/tophat, https://bio.tools/tophat, https://sources.debian.org/src/tophat/ | http://tophat.cbcb.umd.edu/ | SCR_013035 | tophat, TopHat1, Tophat2 | 2026-08-29 11:24:28 | 9789 | ||||
|
Taverna Resource Report Resource Website 10+ mentions |
Taverna (RRID:SCR_004437) | Taverna | data processing software, software application, software resource, workflow software | An open source and domain independent Workflow Management System ����?? a suite of tools used to design and execute scientific workflows and aid in silico experimentation. Taverna Workbench now has support for service sets, offline workflow editing, workflow validation, improved workflow run monitoring, and the pausing and canceling of workflow runs. The command line tool allows you to run workflows outside of the workbench and is available as a stand-alone download or bundled with the Taverna Workbench 2.2.0 download. The Taverna suite is written in Java and includes the Taverna Engine (used for enacting workflows) that powers both the Taverna Workbench (the desktop client application) and the Taverna Server (which allows remote execution of workflows). Taverna is also available as a Command Line Tool for a quick execution of workflows from a terminal. Taverna 2.2.0 includes * Copy/paste, shortcuts, undo/redo, drag and drop * Animated workflow diagram * Remembers added/removed services * Secure Web services support * Secure access to resources on the web * Up-to-date R support * Intermediate values during workflow runs * myExperiment integration * Excel and csv spreadsheet support * Command line tool |
is listed by: OMICtools is listed by: SoftCite is related to: myExperiment is related to: U-Compare is related to: Taverna Knowledge Blog is related to: AIDA Toolkit is related to: Knowledge Blog has parent organization: University of Manchester; Manchester; United Kingdom |
OMII-UK ; EPSRC ; BBSRC ; Microsoft ; ESRC ; JISC |
PMID:18337261 PMID:23640334 |
Open unspecified license | nlx_43462, OMICS_01146 | SCR_004437 | 2026-08-29 11:22:04 | 30 | |||||||
|
STAR Resource Report Resource Website 10000+ mentions |
STAR (RRID:SCR_004463) | alignment software, data processing software, image analysis software, software application, software resource | Software performing alignment of high-throughput RNA-seq data. Aligns RNA-seq reads to reference genome using uncompressed suffix arrays. | RNA-seq data, alignment, RNA-seq reads alignment, reference genome, using uncompressed suffix arrays, bio.tools |
is used by: STARsolo is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
NHGRI U54 HG004557 | PMID:23104886 DOI:10.1093/bioinformatics/bts635 |
biotools:star, OMICS_01254, SCR_015899 | https://github.com/alexdobin/STAR, https://bio.tools/star, https://sources.debian.org/src/rna-star/ | SCR_004463 | Spliced Transcripts Alignment to Reference, Spliced Transcripts Alignment to a Reference (STAR), rna-star, ultrafast universal RNA-seq aligner | 2026-08-29 11:22:05 | 26381 | ||||||
|
Primer Designer Resource Report Resource Website 1+ mentions |
Primer Designer (RRID:SCR_003189) | Primer Designer | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Software program to aid in designing of primers and creation of primer sheets. The program allows users to select a background and enter mutaions. An initial primer is then suggested. User can manipulate the selected primer to add or remove nucleotides from either 5? or 3? ends. A set of parameters reflecting the goodness of the primer is updated on the fly, as the user makes changes. Once happy with the primer, the information is saved in a primer sheet, which can then be uploaded to the BGME lab primer database on the Wiki. | primer, primer design |
is listed by: OMICtools is listed by: SoftCite |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02327 | https://www.thermofisher.com/us/en/home/life-science/oligonucleotides-primers-probes-genes/custom-dna-oligos/oligo-design-tools.html?ef_id=Cj0KCQjw-NfDBhDyARIsAD-ILeBszOXU4wXumqZJ--N8Z5rguB5P2-7UmpEuidzHsK1sgSXJROQ3of8aAtkqEALw_wcB:G:s&s_kwcid=AL!3652!3!683518170873!e!!g!!primer%20designer!20841448243!155985486683&cid=bid_mol_pch_r01_co_cp1358_pjt0000_bid00000_0se_gaw_nt_pur_con&gad_source=1&gad_campaignid=20841448243&gbraid=0AAAAADxi_GTCU-6xCgQrctnmtmtMSDEQj&gclid=Cj0KCQjw-NfDBhDyARIsAD-ILeBszOXU4wXumqZJ--N8Z5rguB5P2-7UmpEuidzHsK1sgSXJROQ3of8aAtkqEALw_wcB | SCR_003189 | 2026-08-29 11:21:46 | 2 | |||||||
|
Primer3 Resource Report Resource Website 10000+ mentions |
Primer3 (RRID:SCR_003139) | Primer3 | analysis service resource, data analysis service, production service resource, service resource, software resource | Tool used to design PCR primers from DNA sequence - often in high-throughput genomics applications. It does everything from mispriming libraries to sequence quality data to the generation of internal oligos. | primer, primer design, polymerase chain reaction, pcr primer, dna sequence, c, perl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Primer3Plus is related to: Primer-BLAST has parent organization: University of Tartu; Tartu; Estonia |
NHGRI R01-HG00257; NHGRI P50-HG00098 |
PMID:22730293 PMID:17379693 DOI:10.1385/1-59259-192-2:365 DOI:10.1385/1-59259-192-2:365 |
Free, Freely available | nlx_156833, OMICS_02325, biotools:primer3 | http://bioinfo.ut.ee/primer3-0.4.0/, http://sourceforge.net/projects/primer3/, http://frodo.wi.mit.edu/primer3, https://bio.tools/primer3, https://sources.debian.org/src/primer3/, https://sources.debian.org/src/primer3/ | SCR_003139 | Primer3web - Pick primers from a DNA sequence, Primer3 - PCR primer design tool, Primer3web | 2026-08-29 11:21:26 | 11934 |
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