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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
beadarray Resource Report Resource Website 100+ mentions |
beadarray (RRID:SCR_001314) | beadarray | software resource | Software package to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided. | microarray, quality control, one channel, preprocessing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Bioconductor |
PMID:17586828 | GNU General Public License, v2 | OMICS_02021, biotools:beadarray | https://bio.tools/beadarray | SCR_001314 | beadarray - Quality assessment and low-level analysis for Illumina BeadArray data | 2026-09-03 04:44:28 | 123 | |||||
|
FACS Resource Report Resource Website 1+ mentions |
FACS (RRID:SCR_000055) | FACS | software resource | Software for classification of Sequences using Bloom filters that can accurately and rapidly align sequences to a reference sequence. | unix/linux, sequence, bio.tools |
is listed by: OMICtools is listed by: GitHub is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: SciLifeLab |
PMID:20472541 | Free, Available for download, Freely available | OMICS_02147, biotools:facs | https://bio.tools/facs | SCR_000055 | Fast and Accurate Classification of Sequences | 2026-09-03 04:43:07 | 6 | |||||
|
Glide Resource Report Resource Website 10+ mentions |
Glide (RRID:SCR_000187) | Glide | simulation software, software application, software resource | Software package which approximates a complete search of the conformational, orientational, and positional space of the ligand in a given receptor. Used in drug development for predicting protein ligand binding modes and ranking ligands via high throughput virtual screening. | ligand, receptor, docking, computation, virtual, screening, drug, discovery |
is listed by: OMICtools is listed by: SoftCite has parent organization: Schrodinger works with: Ligprep |
PMID:18428795 | Restricted | OMICS_01601 | SCR_000187 | 2026-09-03 04:43:21 | 17 | |||||||
|
GOLD Resource Report Resource Website 10+ mentions |
GOLD (RRID:SCR_000188) | GOLD | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software for virtual screening and identifying the binding mode of active molecules. It is comprehensively validated, widely used, and allows for high database enrichments. The software utilizes a novel methodology which avoids computationally expensive sequential docking of ligands into multiple protein structures. | virtual screening, binding, active molecules, ligand-protein bonding, computation, protein structures, lead optimization |
is listed by: OMICtools is listed by: SoftCite |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01602 | SCR_000188 | 2026-09-03 04:43:20 | 18 | ||||||||
|
ProteinProphet Resource Report Resource Website 10+ mentions |
ProteinProphet (RRID:SCR_000286) | software resource | Software that automatically validates protein identifications made on the basis of peptides assigned to MS/MS spectra by database search programs such as SEQUEST. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: SourceForge |
PMID:14632076 | OMICS_02521, biotools:proteinprophet | https://bio.tools/proteinprophet | SCR_000286 | 2026-09-03 04:43:29 | 11 | ||||||||
|
GraphPad Resource Report Resource Website 1000+ mentions |
GraphPad (RRID:SCR_000306) | commercial organization | A commercial graphing software company that offers scientific software for statistical analyses, curve fitting and data analysis. It offers four programs: Prism, InStat, StatMate and QuickCalcs. | company, data, graph, scientific, statistical, analysis, curve, fitting |
is listed by: SoftCite is parent organization of: GraphPad Prism |
Restricted | nlx_156835 | SCR_000306 | 2026-09-03 04:43:29 | 1320 | |||||||||
|
IGOR Pro Resource Report Resource Website 500+ mentions |
IGOR Pro (RRID:SCR_000325) | authoring tool, data analysis software, data processing software, data visualization software, software application, software resource | Software used for visualizing and graphing data, image processing, and programming. It is designed for use by scientists and engineers and supports large data sets, evenly spaced data, and various data import formats. The software includes a suite of image processing operations for image filtering, manipulation, and quantification and is completely programmable. | commercial tool, electrophysiology, authoring tool, data visualization software, image processing, publication quality, interactive | is listed by: SoftCite | Restricted | nlx_156887, SCR_014216 | SCR_000325 | Igor Pro - Technical graphing and data analysis, Igor Software | 2026-09-03 04:43:30 | 680 | ||||||||
|
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 | 2026-09-03 04:43:37 | 1191 | ||||||
|
PRISM (Stanford database) Resource Report Resource Website 10000+ mentions |
PRISM (Stanford database) (RRID:SCR_005375) | PRISM | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5,2022.Tool that predicts interactions between transcription factors and their regulated genes from binding motifs. Understanding vertebrate development requires unraveling the cis-regulatory architecture of gene regulation. PRISM provides accurate genome-wide computational predictions of transcription factor binding sites for the human and mouse genomes, and integrates the predictions with GREAT to provide functional biological context. Together, accurate computational binding site prediction and GREAT produce for each transcription factor: 1. putative binding sites, 2. putative target genes, 3. putative biological roles of the transcription factor, and 4. putative cis-regulatory elements through which the factor regulates each target in each functional role., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | genomic, transcription factor, function, transcription factor binding site, transcription factor regulator, biological role, target gene, target genomic region, genome, FASEB list |
is listed by: OMICtools is listed by: SoftCite is related to: GREAT: Genomic Regions Enrichment of Annotations Tool has parent organization: Stanford University School of Medicine; California; USA |
PMID:23382538 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00489 | SCR_005375 | Predicting Regulatory Information from Single Motifs | 2026-09-03 04:47:53 | 40822 | ||||||
|
Kepler Resource Report Resource Website 10+ mentions |
Kepler (RRID:SCR_005252) | Kepler | data processing software, software application, software resource, workflow software | Kepler is a software application for analyzing and modeling scientific data. Using Kepler''s graphical interface and components, scientists with little background in computer science can create executable models, called scientific workflows, for flexibly accessing scientific data (streaming sensor data, medical and satellite images, simulation output, observational data, etc.) and executing complex analyses on this data. Kepler is developed by a cross-project collaboration led by the Kepler/CORE team. The software builds upon the mature Ptolemy II framework, developed at the University of California, Berkeley. Ptolemy II is a software framework designed for modeling, design, and simulation of concurrent, real-time, embedded systems. The Kepler Project is dedicated to furthering and supporting the capabilities, use, and awareness of the free and open source, scientific workflow application, Kepler. Kepler is designed to help scien��tists, analysts, and computer programmers create, execute, and share models and analyses across a broad range of scientific and engineering disciplines. Kepler can operate on data stored in a variety of formats, locally and over the internet, and is an effective environment for integrating disparate software components, such as merging R scripts with compiled C code, or facilitating remote, distributed execution of models. Using Kepler''s graphical user interface, users simply select and then connect pertinent analytical components and data sources to create a scientific workflowan executable representation of the steps required to generate results. The Kepler software helps users share and reuse data, workflows, and compo��nents developed by the scientific community to address common needs. Kepler is a java-based application that is maintained for the Windows, OSX, and Linux operating systems. The Kepler Project supports the official code-base for Kepler development, as well as provides materials and mechanisms for learning how to use Kepler, sharing experiences with other workflow developers, reporting bugs, suggesting enhancements, etc. The Kepler Project Leadership Team works to assure the long-term technical and financial viability of Kepler by making strategic decisions on behalf of the Kepler user community, as well as providing an official and durable point-of-contact to articulate and represent the interests of the Kepler Project and the Kepler software application. Details about how to get more involved with the Kepler Project can be found in the developer section of this website. | software, workflow |
is listed by: SoftCite is related to: bioKepler has parent organization: University of California at Davis; California; USA has parent organization: University of California at Santa Barbara; California; USA has parent organization: University of California at San Diego; California; USA |
NSF 0722079 | nlx_144278 | SCR_005252 | Kepler Project | 2026-09-03 04:47:55 | 49 | |||||||
|
BioExtract Resource Report Resource Website 10+ mentions |
BioExtract (RRID:SCR_005397) | BioExtract | service resource | An open, web-based system designed to aid researchers in the analysis of genomic data by providing a platform for the creation of bioinformatic workflows. Scientific workflows are created within the system by recording tasks performed by the user. These tasks may include querying multiple, distributed data sources, saving query results as searchable data extracts, and executing local and web-accessible analytic tools. The series of recorded tasks can then be saved as a reproducible, sharable workflow available for subsequent execution with the original or modified inputs and parameter settings. Integrated data resources include interfaces to the National Center for Biotechnology Information (NCBI) nucleotide and protein databases, the European Molecular Biology Laboratory (EMBL-Bank) non-redundant nucleotide database, the Universal Protein Resource (UniProt), and the UniProt Reference Clusters (UniRef) database. The system offers access to numerous preinstalled, curated analytic tools and also provides researchers with the option of selecting computational tools from a large list of web services including the European Molecular Biology Open Software Suite (EMBOSS), BioMoby, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The system further allows users to integrate local command line tools residing on their own computers through a client-side Java applet. | nucleotide sequence, protein sequence, viridiplantae, viridiplantae protein, nucleotide, sequence, protein, viridiplantae, workflow, software, database, bioinformatics, platform, genome, genomic analysis, analytic tool |
is listed by: OMICtools is listed by: SoftCite is related to: NCBI Nucleotide is related to: NCBI Protein Database is related to: UniProt is related to: UniRef is related to: EMBOSS is related to: BioMoby is related to: KEGG has parent organization: Indiana University; Indiana; USA has parent organization: University of South Dakota; South Dakota; USA |
NSF 0090732; NSF IOS-1126481 |
PMID:21546552 PMID:20865520 PMID:20150665 PMID:20054995 |
OMICS_01138 | SCR_005397 | BioExtract Server | 2026-09-03 04:48:01 | 12 | ||||||
|
Hmmer Resource Report Resource Website 5000+ mentions |
Hmmer (RRID:SCR_005305) | HMMER | analysis service resource, data analysis service, data analysis software, data processing software, production service resource, service resource, software application, software resource | Tool for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST. | homolog, protein sequence, source code, FASEB list |
is used by: Mantis is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: Debian is listed by: SoftCite is related to: VectorBase has parent organization: Janelia Research |
Howard Hughes Medical Institute | PMID:21593126 DOI:10.1093/bioinformatics/14.9.755 |
OMICS_00996, nlx_144358 | https://sources.debian.org/src/hmmer/ | SCR_005305 | HMMER - biosequence analysis using profile hidden Markov models | 2026-09-03 04:48:14 | 9520 | |||||
|
Hydra Resource Report Resource Website 100+ mentions |
Hydra (RRID:SCR_005260) | Hydra | software resource | Software that detects structural variation (SV) breakpoints by clustering discordant paired-end alignments whose signatures corroborate the same putative breakpoint. Hydra can detect breakpoints caused by all classes of structural variation. Moreover, it was designed to detect variation in both unique and duplicated genomic regions; therefore, it will examine paired-end reads having multiple discordant alignments. Hydra does not attempt to classify SV breakpoints based on the mapping distances and orientations of each breakpoint cluster, it merely detects and reports breakpoints. This is an intentional decision, as it was observed that in loci affected by complex rearrangements, the type of variant suggested by the breakpoint signature is not always correct. Hydra does report the orientations, distances, number of supporting read-pairs, etc., for each breakpoint. It is suggested that downstream methods be used to classify variants based on the genomic features that they overlap and the co-occurrence of other breakpoints. For example, they developed BEDTools for exactly this purpose and the breakpoints reported by Hydra are in the BEDPE format used by BEDTools. Future releases of Hydra will include scripts that assist in the classification process. | structural variation, genome, genomic, breakpoint, c++, cnv, pem, paired-end, segmental duplication, rearrangement |
is listed by: OMICtools is listed by: SoftCite is related to: BEDTools has parent organization: Google Code has parent organization: University of Virginia; Virginia; USA |
OMICS_00318 | SCR_005260 | hydra-sv | 2026-09-03 04:48:10 | 119 | ||||||||
|
PASS Resource Report Resource Website 1000+ mentions |
PASS (RRID:SCR_005490) | PASS | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 19, 2020.A program to align short sequences that has been developed with an innovative strategy to perform fast gapped and ungapped alignment onto a reference sequence. It supports several data formats and allows the user to modulate very finely the sensitivity of the alignments. The program is designed to handle huge amounts of short reads generated by ILLUMINA, SOLiD and Roche-454 technology. The optimization of the internal data structure and a filter based on precomputed short-word alignments allow the program to skip false positives in the extension phase, thus reducing the execution time without loss of sensitivity. The final alignment is performed by dynamic programming., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: PASS-bis has parent organization: University of Padua; Padua; Italy |
PMID:19218350 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:pass, OMICS_00673 | https://bio.tools/pass | SCR_005490 | PASS: a program to align short sequences | 2026-09-03 04:47:58 | 2085 | |||||
|
Maq Resource Report Resource Website 50+ mentions |
Maq (RRID:SCR_005485) | Maq | software resource | A set of programs that map and assemble fixed-length Solexa/SOLiD reads in a fast and accurate way. | command-line, curses/ncurses, opengl, c, c++, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: SourceForge |
DOI:10.1101/gr.078212.108 | GNU General Public License, v2 | OMICS_00668, biotools:maq | https://bio.tools/maq, https://sources.debian.org/src/maq/ | SCR_005485 | mapass2, Mapping and Assembly with Quality, Mapping and Assembly with Qualities, Maq: Mapping and Assembly with Qualities | 2026-09-03 04:48:06 | 74 | |||||
|
Bowtie Resource Report Resource Website 10000+ mentions |
Bowtie (RRID:SCR_005476) | alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource | Software ultrafast memory efficient tool for aligning sequencing reads. Bowtie is short read aligner. | sequence, analysis, long, reference, read, alignment, gap, local, pair, end, rna, rnaseq, bio.tools |
is used by: deFuse is used by: Short Read Sequence Typing for Bacterial Pathogens is used by: TopHat is used by: BS Seeker is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Bowtie 2 has parent organization: Johns Hopkins University; Maryland; USA is required by: RelocaTE |
Amazon Web Services in Education Research ; NHGRI R01 HG006102; NIGMS R01 GM083873 |
PMID:19261174 DOI:10.1186/gb-2009-10-3-r25 |
Free, Available for download, Freely available | biotools:bowtie, OMICS_00653 | https://github.com/BenLangmead/bowtie, https://bio.tools/bowtie, https://sources.debian.org/src/bowtie/ | SCR_005476 | 2026-09-03 04:48:05 | 13799 | ||||||
|
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 | 2026-09-03 04:48:39 | 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 | 2026-09-03 04:48:06 | 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 | 2026-09-03 04:48:14 | 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 | 2026-09-03 04:48:29 | 3544 |
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