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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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DAGitty Resource Report Resource Website 10+ mentions |
DAGitty (RRID:SCR_024509) | software toolkit, software resource | Software R package provides access to all of the capabilities of DAGitty web application for drawing and analysing Directed Acyclic Graphs within the R platform for statistical computing. Used for graphical analysis of structural causal models. | graphical analysis of structural causal models, drawing and analysing Directed Acyclic Graphs, | is listed by: SoftCite | PMID:28089956 | Free, Available for download, Freely available | https://github.com/jtextor/dagitty | SCR_024509 | 2026-02-15 09:23:45 | 18 | ||||||||
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FastMulRFS Resource Report Resource Website 1+ mentions |
FastMulRFS (RRID:SCR_024505) | software toolkit, software resource | Software pipeline for estimating species trees from multi copy gene trees. | estimating species trees, multi copy gene trees, | is listed by: SoftCite | PMID:32657396 | Free, Available for download, Freely available | SCR_024505 | 2026-02-15 09:23:45 | 1 | |||||||||
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NOTUNG Resource Report Resource Website 1+ mentions |
NOTUNG (RRID:SCR_024484) | software toolkit, software resource | Software package to facilitate large scale analysis, using both rooted and unrooted trees.Used for dating gene duplications and optimizing gene family trees.Used for inferring duplication dates from gene trees automatically and can also be used as exploratory analysis tool for evaluating alternative hypotheses. | inferring duplication dates, large scale analysis, dating gene duplications, optimizing gene family trees, | is listed by: SoftCite | PMID:11108472 | Free, Available for download, Freely available | SCR_024484 | Notung 2.9 | 2026-02-15 09:23:30 | 9 | ||||||||
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CMplot Resource Report Resource Website 50+ mentions |
CMplot (RRID:SCR_024514) | software toolkit, software resource | Software drawing R package designed for Manhattan plot of genomic analysis. | drawing tool, Manhattan plot of genomic analysis, | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/YinLiLin/CMplot | SCR_024514 | Circle Manhattan Plot | 2026-02-15 09:22:43 | 56 | ||||||||
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maftools Resource Report Resource Website 100+ mentions |
maftools (RRID:SCR_024519) | software toolkit, software resource | Software R package offers multitude of analysis and visualization modules that are commonly used in cancer genomic studies, including driver gene identification, pathway, signature, enrichment, and association analyses. Maftools requires somatic variants in Mutation Annotation Format (MAF) and is independent of larger alignment files. | MAF summarize, MAF analyze, MAF visualize, Mutation Annotation Format files, driver gene identification, pathway, signature, enrichment, association analyses, somatic variants in Mutation Annotation Format, MAF | is listed by: SoftCite | PMID:30341162 | Free, Available for download, Freely available | https://bioconductor.org/packages/maftools/ | SCR_024519 | 2026-02-15 09:23:34 | 195 | ||||||||
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Treerecs Resource Report Resource Website 1+ mentions |
Treerecs (RRID:SCR_024497) | software application, software resource | Open source, species and gene tree reconciliation software. Software integrated phylogenetic tool, from sequences to reconciliations. Used to correct, rearrange and reroot gene trees with regard to given species tree. | species and gene tree reconciliation, integrated phylogenetic, from sequences to reconciliations, correct gene trees, rearrange gene trees, reroot gene trees, | is listed by: SoftCite | PMID:33085745 | Free, Available for download, Freely available | https://project.inria.fr/treerecs/ | SCR_024497 | 2026-02-15 09:23:45 | 1 | ||||||||
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X!Tandem Resource Report Resource Website 10+ mentions |
X!Tandem (RRID:SCR_015645) | software application, data processing software, data analysis software, software resource | Software tool that can match tandem mass spectra with peptide sequences, in process known as protein identification. Database search engine for matching tandem mass spectra with protein sequences. Command line tool for matching tandem mass spectra with peptide sequences. | Search engine, command line tool, matching tandem mass spectra, peptide sequence, protein sequence, protein identification, tandem mass spectrum, xml file, FASEB list |
is listed by: SoftCite is related to: XTandem Parser |
Free, Available for download, Freely available | SCR_018388 | SCR_015645 | 2026-02-15 09:21:34 | 44 | |||||||||
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JASP Resource Report Resource Website 1000+ mentions |
JASP (RRID:SCR_015823) | software application, data processing software, data analysis software, software resource | Statistics software that performs common frequentist analyses and Bayesian analyses. It conducts ANOVA, linear regression, and correlation, among other statistical tests. | statistical analysis, data analysis, statistical test, frequentist analysis, bayesian analysis, r package |
uses: R Project for Statistical Computing is listed by: SoftCite |
European Research Council | PMID:28685272 | Open source, Free, Available for download, Tutorial available, Runs on Windows, Runs on MAC OS, Runs on Linux | https://github.com/jasp-stats/jasp-desktop | SCR_015823 | 2026-02-15 09:20:58 | 3851 | |||||||
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BLASTX Resource Report Resource Website 10000+ mentions |
BLASTX (RRID:SCR_001653) | BLASTX | data analysis service, analysis service resource, database, production service resource, service resource, data or information resource | Web application to search protein databases using a translated nucleotide query. Translated BLAST services are useful when trying to find homologous proteins to a nucleotide coding region. Blastx compares translational products of the nucleotide query sequence to a protein database. Because blastx translates the query sequence in all six reading frames and provides combined significance statistics for hits to different frames, it is particularly useful when the reading frame of the query sequence is unknown or it contains errors that may lead to frame shifts or other coding errors. Thus blastx is often the first analysis performed with a newly determined nucleotide sequence and is used extensively in analyzing EST sequences. This search is more sensitive than nucleotide blast since the comparison is performed at the protein level. | protein, translated nucleotide, blast, nucleotide, expressed sequence tag, sequence, genome, wgs, peptide, alignment, dna |
is listed by: OMICtools is listed by: SoftCite has parent organization: NCBI |
PMID:28902395 PMID:8485583 |
Free, Freely Available | nlx_153933, OMICS_00992 | http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastx&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome | SCR_001653 | Translated BLAST, Translated BLAST: blastx | 2026-02-16 09:45:32 | 10091 | |||||
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ASAP Resource Report Resource Website 50+ mentions |
ASAP (RRID:SCR_001849) | ASAP | data repository, database, storage service resource, service resource, data or information resource | Database and web interface developed to store, update and distribute genome sequence data and gene expression data. ASAP was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis. The ASAP database includes multiple genome sequences at various stages of analysis, and gene expression data from preliminary experiments. Use of some of this preliminary data is conditional, and it is the users responsibility to read the data release policy and to verify that any use of specific data obtained through ASAP is consistent with this policy. There are four main routes to viewing the information in ASAP: # a summary page, # a form to query the genome annotations, # a form to query strain collections, and # a form to query the experimental data. Navigational buttons appear on every page allowing users to jump to any of these four points., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene expression, genome, genome sequence, multiple genome sequence, post sequencing functional analysis, preliminary experiment, blast, annotation, data analysis service |
is used by: NIF Data Federation is listed by: SoftCite is related to: AmiGO has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
USDA 2001-52100-11316; NIGMS GM62994-02; NIGMS GM35682-15A1 |
PMID:12519969 | Free, Freely available | nif-0000-02571 | https://omictools.com/asap-3-tool | SCR_001849 | A Systematic Annotation Package for Community Analysis of Genome, ASAP: a systematic annotation package for community analysis of genomes, A systematic annotation package for community analysis of genomes | 2026-02-16 09:45:36 | 53 | ||||
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DAVID Resource Report Resource Website 10000+ mentions |
DAVID (RRID:SCR_001881) | DAVID | web service, data access protocol, database, software resource, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. Bioinformatics resource system including web server and web service for functional annotation and enrichment analyses of gene lists. Consists of comprehensive knowledgebase and set of functional analysis tools. Includes gene centered database integrating heterogeneous gene annotation resources to facilitate high throughput gene functional analysis. | functional domain, annotation, motif, protein, ontology enrichment, gene, high-throughput, functional classification, functional annotation, clustering, genome, pathway, gene-disease association, interaction, functional domain, motif, visualization, FASEB list |
is listed by: OMICtools is listed by: 3DVC is listed by: LabWorm is listed by: SoftCite is related to: Gene Ontology is related to: BioCarta Pathways is related to: KEGG has parent organization: NCI-Frederick |
NIAID NO1-CO-56000; NCI |
PMID:19131956 PMID:12734009 PMID:35325185 PMID:22543366 PMID:17980028 PMID:17576678 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30408, nif-0000-10451, OMICS_02220, SCR_003033 | http://david.abcc.ncifcrf.gov/ | SCR_001881 | DAVID Bioinformatics Resources, Visualization and Integrated Discovery Bioinformatics Resources, Database for Annotation Visualization and Integrated Discovery, The Database for Annotation, The Database for Annotation Visualization and Integrated Discovery Bioinformatics Resources | 2026-02-16 09:45:36 | 18488 | ||||
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GATK Resource Report Resource Website 10000+ mentions |
GATK (RRID:SCR_001876) | GATK | software application, data processing software, software toolkit, data analysis software, software library, software resource | A software package to analyze next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. This software library makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner. (entry from Genetic Analysis Software) | gene, genetic, genomic, next-generation resequencing, bio.tools |
is used by: Halvade Somatic is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: SnpEff has parent organization: Broad Institute |
PMID:21478889 | Free, Available for download, Freely available | nlx_154324, OMICS_00286, biotools:gatk | http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit https://bio.tools/gatk |
SCR_001876 | Genome Analysis ToolKit | 2026-02-16 09:45:36 | 16663 | |||||
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RMS Resource Report Resource Website 1+ mentions |
RMS (RRID:SCR_007415) | RMS | training resource, topical portal, job resource, portal, data or information resource | It is at the forefront of new ideas and developments in microscopy and imaging. The RMS is the only truly international microscopical society, drawing distinguished members from all over the world. It also serves the needs of its company members who represent all the major manufacturers and suppliers of microscopes, equipment and services. In addition to this, the Society is pursuing an initiative to encourage young microscope users who may go on to influence microscopy in years to come. The Society is dedicated to advancing science, developing careers and supporting wider understanding of science and microscopy through its Science and Society activities. In support of the above, it publishes The Journal of Microscopy and microscopy handbooks, as well as helping young scientists through bursaries. The Society is incorporated by Royal Charter. Its governing documents are its Charter and By-laws. The most recent AGM minutes, Trustees Report and Accounts are available below - 2007 AGM draft minutes Full 2007 Trustees Report and Accounts - as submitted to the Charity Commission The RMS is a member of: - the Foundation for Science and Technology - the Biosciences Federation - the International Federation of Societies for Microscopy - the European Microscopy Society training opportunities; jobs. | is listed by: SoftCite | nif-0000-00498 | SCR_007415 | The Royal Microscopical Society | 2026-02-16 09:46:58 | 6 | |||||||||
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WFU PickAtlas Resource Report Resource Website 1000+ mentions |
WFU PickAtlas (RRID:SCR_007378) | PickAtlas | data processing software, software application, software resource, image processing software | A software toolbox that provides a method for generating Region of Interest (ROI) masks based on the Talairach Daemon database. The atlases include Brodmann area, Lobar, Hemisphere, Anatomic Label (gyral anatomy), and Tissue type. The atlases have been extended to the vertex in MNI space, and corrected for the precentral gyrus anomaly. Additional atlases (including non-human atlases) can be added without difficulty., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | neuroanatomy, cytoarchitecture, fmri, matlab, brain, brain region, talairach daemon, analyze, atlas application, matlab, microsoft, magnetic resonance, posix/unix-like, win32 (ms windows), windows, FASEB list |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: SoftCite is related to: Talairach Daemon has parent organization: Wake Forest School of Medicine; North Carolina; USA |
NIBIB 1R03EB008670 | PMID:12880848 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00358 | SCR_007378 | WFU_PickAtlas | 2026-02-16 09:46:57 | 1261 | |||||
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CCP4 Resource Report Resource Website 1000+ mentions |
CCP4 (RRID:SCR_007255) | CCP4 | software application, data processing software, data analysis software, portal, software resource, simulation software, service resource, data or information resource | Portal for Macromolecular X-Ray Crystallography to produce and support an integrated suite of programs that allows researchers to determine macromolecular structures by X-ray crystallography, and other biophysical techniques. Used in the education and training of scientists in experimental structural biology for determination and analysis of protein structure. | macromolecular, x-ray, crystallography, biophysical, technique, structural, biology, analysis, protein, Research Complex at Harwell, computational, collaborative, project |
is used by: MoRDa is used by: PDB-REDO is listed by: SoftCite is related to: BALBES is related to: CCP4mg is related to: fragon is related to: ConPlot has parent organization: Science and Technology Facilities Council |
Science and Technology Facilities Council | Free, Available for download, Freely available, Tutorial available | SCR_016709, nif-0000-30238 | SCR_007255 | The Collaborative Computational Project Number 4 in Protein Crystallography, Collaborative Computational Project Number 4 | 2026-02-16 09:46:55 | 4740 | ||||||
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Imaris Resource Report Resource Website 10000+ mentions |
Imaris (RRID:SCR_007370) | image analysis software, data processing software, software application, software resource | Imaris provides range of capabilities for working with three dimensional images. Uses flexible editing and processing functions, such as interactive surface rendering and object slicing capabilities. And output to standard TIFF, Quicktime and AVI formats. Imaris accepts virtually all image formats that are used in confocal microscopy and many of those used in wide-field image acquisition. Imaris version 10.1 for image analysis workflows using AI trainable object detection. | Three dimensional images, 3D image, AI trainable object detection, |
is used by: Simple Assignment of Spots to Surfaces is listed by: SoftCite is related to: FilamentTracer is related to: ImarisViewer |
Restricted | nif-0000-00314 | https://imaris.oxinst.com/ https://imaris.oxinst.com/newrelease |
SCR_007370 | , Imaris 10.1, Imaris 9.7 | 2026-02-16 09:46:57 | 15762 | |||||||
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BioEdit Resource Report Resource Website 10000+ mentions |
BioEdit (RRID:SCR_007361) | software application, data processing software, sequence analysis software, data analysis software, image analysis software, software resource, alignment software | Software tool as biological sequence alignment editor written for Windows 95/98/NT/2000/XP/7 and sequence analysis program. Provides sequence manipulation and analysis options and links to external analysis programs to view and manipulate sequences with simple point and click operations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequence, alignment, editor, analysis, program | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156845 | SCR_007361 | 2026-02-16 09:46:57 | 13339 | |||||||||
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Simulink Resource Report Resource Website 100+ mentions |
Simulink (RRID:SCR_014744) | software application, software resource, simulation software, software toolkit | Block diagram environment that contains a graphical editor, customizable block libraries, and solvers for multidomain simulation and model-based design in MATLAB. It supports simulation, automatic code generation, and continuous test and verification of embedded systems. | matlab, block diagram, multidomain simulation, simulation software, model based design, automatic code generation | is listed by: SoftCite | Commercially available, Free trial available | SCR_014744 | 2026-02-16 09:48:41 | 364 | ||||||||||
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ProtTest Resource Report Resource Website 1000+ mentions |
ProtTest (RRID:SCR_014628) | software application, data processing software, data analysis software, software resource, web application | Web-based software used for the selection of best-fit models of protein evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bioinformatics, model, best fit model, protein evolution, amino acid replacement, server, bio.tools |
uses: PhyML is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite is hosted by: GitHub |
PMID:15647292 DOI:10.1093/bioinformatics/btr088 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_11547, biotools:prottest | https://github.com/ddarriba/prottest3 https://bio.tools/prottest https://sources.debian.org/src/prottest/ |
SCR_014628 | 2026-02-16 09:48:39 | 1981 | |||||||
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IUPRED Resource Report Resource Website 100+ mentions |
IUPRED (RRID:SCR_014632) | software application, data processing software, sequence analysis software, data analysis software, software resource, web application | A web server which recognizes tertiary structures from an amino acid sequence based on estimated pairwise energy content. Users can input SWISS-PROT/TrEMBL identifier or accession number, or paste the amino acid sequence. | web application, sequence analysis, web server, territory structure, amino acid sequence, swiss prot, trembl | is listed by: SoftCite | PMID:15955779 | Available to academic users, Available for download, Commercial users must enquire | SCR_014632 | Prediction of Intrinsically Unstructured Proteins, Prediction of Intrinsically Unstructured Proteins (IUPRED) | 2026-02-16 09:48:39 | 295 |
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