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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Clustal W2 Resource Report Resource Website 5000+ mentions |
Clustal W2 (RRID:SCR_002909) | software application, service resource, software resource, data processing software, alignment software, image analysis software | THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022. Command line version of multiple sequence alignment program Clustal for DNA or proteins. Alignment is progressive and considers sequence redundancy. No longer being maintained. Please consider using Clustal Omega instead which accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/ClustalW, GCG/MSF, RSF. | multiple, sequence, alignment, cladogram, phylogram, evolution, phylogenetic, tree, protein, nucleic, acid, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite is related to: Clustal Omega is related to: UniProt is related to: Clustal Omega is related to: VectorBase is related to: TopoSNP is related to: Clustal 2 has parent organization: European Bioinformatics Institute has parent organization: University College Dublin; Dublin; Ireland |
Science Foundation Ireland | PMID:17846036 PMID:20439314 DOI:10.1093/bioinformatics/btm404 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02562, nif-0000-30076 | http://www.ch.embnet.org/software/ClustalW.html, https://sources.debian.org/src/clustalx/ | http://www.ebi.ac.uk/tools/clustalw/ | SCR_002909 | European Bioinformatics Institute - ClustalW2 | 2026-07-28 09:40:34 | 7830 | ||||
|
Gene Set Enrichment Analysis Resource Report Resource Website 10000+ mentions |
Gene Set Enrichment Analysis (RRID:SCR_003199) | GSEA | software application, data analysis software, software resource, data processing software, software toolkit | Software package for interpreting gene expression data. Used for interpretation of a large-scale experiment by identifying pathways and processes. | gene, expression, profile, pathway, data, set, phenotype, genome, enrichment, RNA, analysis, bio.tools, bio.tools |
is used by: Molecular Signatures Database is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: GoMapMan has parent organization: Broad Institute |
NCI ; NIH ; NIGMS |
PMID:16199517 | Free, Freely available | nif-0000-30629, SCR_016882, biotools:gsea, OMICS_02279 | http://www.broad.mit.edu/gsea, https://bio.tools/gsea | SCR_003199 | GSEA, Gene Set Enrichment Analysis, Gene Set Enrichment Analysis (GSEA) | 2026-07-28 09:40:37 | 18865 | ||||
|
MIPE Resource Report Resource Website 10+ mentions |
MIPE (RRID:SCR_003065) | narrative resource, data or information resource, standard specification, software resource, interchange format | 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 | Minimal Information for PCR Experiments | 2026-07-28 09:40:43 | 31 | |||||||
|
Stacks Resource Report Resource Website 500+ mentions |
Stacks (RRID:SCR_003184) | Stacks | software application, software resource, data analysis software, data processing software | A software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. It was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. | population genomics, genetic map, phylogenetics, genetics, next-generation sequencing, rad-seq, genotype-by-sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Oregon; Oregon; USA |
PMID:23701397 PMID:22384329 DOI:10.1111/mec.12354 |
Free, Available for download, Freely available | OMICS_01567, biotools:stacks | https://bio.tools/stacks, https://sources.debian.org/src/stacks/ | SCR_003184 | 2026-07-28 09:40:37 | 623 | ||||||
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Eukaryotic Linear Motif Resource Report Resource Website 100+ mentions |
Eukaryotic Linear Motif (RRID:SCR_003085) | ELM | service resource, data or information resource, data analysis service, database, production service resource, analysis 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 | Eukarotic Linear Motif resource for Functional Sites in Proteins | 2026-07-28 09:40:43 | 296 | ||||
|
BioJS Resource Report Resource Website 10+ mentions |
BioJS (RRID:SCR_003119) | BioJS | software application, software library, software resource, data visualization software, data processing software, 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 | 2026-07-28 09:40:44 | 22 | ||||
|
Cytoscape Resource Report Resource Website 10000+ mentions |
Cytoscape (RRID:SCR_003032) | software application, data analysis software, software resource, data processing software, data visualization software | 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 | Complex Network Analysis Visualization, Cytoscape 2.6, Cytoscape 3.0 | 2026-07-28 09:40:36 | 23431 | |||||
|
miRBase Resource Report Resource Website 5000+ mentions |
miRBase (RRID:SCR_003152) | miRBase | service resource, data or information resource, data repository, database, naming service, storage service resource | Central online repository for microRNA nomenclature, sequence data, annotation and target prediction.Collection of published miRNA sequences and annotation. | gene, annotation, hairpin, microrna, nomenclature, rna, sequence, target, transcript, unique name, mirna registry, genetics, bio.tools, FASEB list |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: bio.tools is listed by: Debian has parent organization: University of Manchester; Manchester; United Kingdom |
BBSRC ; Wellcome Trust Sanger Institute |
PMID:24275495 PMID:21037258 PMID:20205188 PMID:17991681 PMID:16957372 PMID:16381832 PMID:14681370 |
Free, Available for download, Freely available | SCR_017497, r3d100010670, nif-0000-03134, biotools:mirbase | http://microrna.sanger.ac.uk/, https://bio.tools/mirbase, https://doi.org/10.17616/R3VG8D | SCR_003152 | microRNA database | 2026-07-28 09:40:38 | 9669 | ||||
|
ms lims Resource Report Resource Website 1+ mentions |
ms lims (RRID:SCR_002974) | software application, software resource, data management software | Software that provides a lightweight, portable yet production-grade solution for managing mass spectrometry based proteomics data. | mass spectrometry, proteomics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code |
PMID:20058248 | Free, Available for download, Freely available | OMICS_02547, biotools:ms-lims | https://bio.tools/ms-lims | SCR_002974 | mass spectrometry based proteomics information management system, ms-lims: mass spectrometry based proteomics information management system | 2026-07-28 09:40:42 | 1 | ||||||
|
IMGT/HLA Resource Report Resource Website 100+ mentions |
IMGT/HLA (RRID:SCR_002971) | IMGT HLA, IMGT/HLA | service resource, data or information resource, data repository, database, storage service resource | Database for sequences of the human major histocompatibility complex (HLA) and includes the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. It currently contains 9,310 allele sequences (2013) along with detailed information concerning the material from which the sequence was derived and data on the validation of the sequences. It is established procedure for authors to submit the sequences directly to the IMGT/HLA Database for checking and assignment of an official name prior to publication, this avoids the problems associated with renaming published sequences and the confusion of multiple names for the same sequence. The need for reasonably rapid publication of new HLA allele sequences has necessitated an annual meeting of the WHO Nomenclature Committee for Factors of the HLA System. Additionally they now publish monthly HLA nomenclature updates both in journals and online to provide quick and easy access to new sequence information. The IMGT/HLA Database is part of the international ImMunoGeneTics project. In collaboration with the Imperial Cancer Research Fund (ICRF) and European Bioinformatics Institute (EBI) they have developed an Oracle database to house the HLA sequences in such a way as to allow users to present complex queries about the sequence, sequence features, references, contacts and allele designations to the database via a graphical user interface over the web. The IMGT/HLA Database Submission Tool allows direct submission of sequences to the WHO HLA Nomenclature Committee for Factors of the HLA System. The IMGT/HLA Database provides an FTP site for the retrieval of sequences in a number of pre-formatted files. | alignment, allele, cell, hla, sequence alignment, major histocompatibility complex, nomenclature, blast, immunogenetics, histocompatibility, gene mapping, gene rearrangement, genetic recombination, genetics, gold standard, bio.tools |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: dbMHC has parent organization: European Bioinformatics Institute has parent organization: Anthony Nolan Research Institute has parent organization: IMGT - the international ImMunoGeneTics information system |
EU Biotech grant BIO4CT960037; Anthony Nolan Trust ; Imperial Cancer Research Fund |
PMID:21071412 PMID:10777106 PMID:18838392 |
Creative Commons Attribution-NoDerivs License | nif-0000-03014, biotools:ipd-imgt_hla, r3d100010804 | https://bio.tools/ipd-imgt_hla, https://doi.org/10.17616/R3T31N | SCR_002971 | IMGT HLA, IMGT/HLA DB, IMGT/HLA Database, International ImMunoGeneTics/Human Leukocyte Antigen Database | 2026-07-28 09:40:42 | 279 | ||||
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ISFinder Resource Report Resource Website 1000+ mentions |
ISFinder (RRID:SCR_003020) | ISFinder | analysis service resource, service resource, data or information resource, data repository, data analysis service, database, production 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 | IS Finder, Isfinder | 2026-07-28 09:40:36 | 1047 | |||||
|
XNAT - The Extensible Neuroimaging Archive Toolkit Resource Report Resource Website 50+ mentions |
XNAT - The Extensible Neuroimaging Archive Toolkit (RRID:SCR_003048) | XNAT | software application, source code, software resource, data management software, data processing software | Software platform designed to facilitate common management and productivity tasks for neuroimaging and associated data. | analyze, client application, collaboration, data archive, data management, data sharing, data store, informatics, metadata, middleware, middleware engine, neuroinformatics, open source, productivity task, quality control, sharing, software platform, user interface, workflow, xml schema, neuroimaging, mri, processing, image, clinical, dicom, anonymization, clinical assessment, application, ct, database application, eeg, meg, ecog, java, magnetic resonance, nifti-1, os independent, pet, spect, platform, web environment, FASEB list |
is used by: studyforrest.org is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: MIRIAD is related to: pyxnat is related to: XNAT Extras is related to: XNAT Central is related to: NUNDA is related to: CardioVascular Research Grid (CVRG) is related to: ConnectomeDB is related to: NA-MIC Kit has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
NIBIB R01 EB009352; NIBIB U54 EB005149 |
PMID:17426351 | Free, Available for download, Freely available | nif-0000-00531 | http://www.nitrc.org/projects/xnat, https://sources.debian.org/src/xnat/ | SCR_003048 | Extensible Neuroimaging Archive Toolkit, Extensible Neuroimaging Archive Toolkit (XNAT) | 2026-07-28 09:40:36 | 57 | ||||
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BioImage Suite Resource Report Resource Website 50+ mentions |
BioImage Suite (RRID:SCR_002986) | software application, software resource, data processing software, data visualization software, image processing software, image analysis software | Web applications for analysis of multimodal/multispecies neuroimaging data. Image analysis software package. Has facilities for DTI and fMRI processing. Capabilities for both neuro/cardiac and abdominal image analysis and visualization. Many packages are extensible, and provide functionality for image visualization and registration, surface editing, cardiac 4D multi-slice editing, diffusion tensor image processing, mouse segmentation and registration, and much more. Can be intergrated with other biomedical image processing software, such as FSL, AFNI, and SPM. | Analysis, multimodal, multispecies, neuroimaging, data, DTI, fMRI, processing, visualization, registration, surface, editing, BRAIN Initiative |
is recommended by: BRAIN Initiative is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: 3D Slicer has parent organization: Yale University; Connecticut; USA |
NIBIB R03 EB012969; NIBIB R01 EB006494; NIMH MH114805 |
PMID:21249532 | Free, Available for download, Freely available | nif-0000-30179 | https://sources.debian.org/src/bioimagesuite/, http://www.nitrc.org/projects/bioimagesuite, https://medicine.yale.edu/bioimaging/suite/ | http://bioimagesuite.yale.edu/index.aspx | SCR_002986 | Bioimagesuite Web | 2026-07-28 09:40:42 | 54 | ||||
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BioPerl Resource Report Resource Website 100+ mentions |
BioPerl (RRID:SCR_002989) | BioPerl | narrative resource, data or information resource, source code, software resource, software repository, wiki, software toolkit | BioPerl is a community effort to produce Perl code which is useful in biology. This toolkit of perl modules is useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the bioperl-live repository consist of the core of the functionality of bioperl. Additionally auxiliary modules for creating graphical interfaces (bioperl-gui), persistent storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (Run package), software to automate bioinformatic analyses (bioperl-pipeline) are all available as Git modules in our repository. The BioPerl toolkit provides a library of hundreds of routines for processing sequence, annotation, alignment, and sequence analysis reports. It often serves as a bridge between different computational biology applications assisting the user to construct analysis pipelines. This chapter illustrates how BioPerl facilitates tasks such as writing scripts summarizing information from BLAST reports or extracting key annotation details from a GenBank sequence record. BioPerl includes modules written by Sohel Merchant of the GO Consortium for parsing and manipulating OBO ontologies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | perl, biology, ontology, library, sequence, analysis, computational, application, pipeline, bioinformatics, sequence, annotation, module, life science, python, java, genome, software library, parse, manipulate, bio.tools |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite is related to: Gene Ontology is related to: OBO has parent organization: Duke University; North Carolina; USA has parent organization: European Bioinformatics Institute is required by: RelocaTE |
NIGMS T32 GM07754-22; NHGRI K22 HG00056; NHGRI K22 HG-00064-01; NHGRI HG00739; NHGRI P41HG02223 |
PMID:12368254 DOI:10.1101/gr.361602 |
Free, Available for download, Freely available | OMICS_04849, nif-0000-30188, biotools:bioperl | https://bio.tools/bioperl, https://sources.debian.org/src/bioperl/ | SCR_002989 | 2026-07-28 09:40:35 | 402 | |||||
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MAGE-TAB Resource Report Resource Website 1+ mentions |
MAGE-TAB (RRID:SCR_003222) | MAGE-TAB | data or information resource, narrative resource, standard specification | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 27,2023. A simple tab-delimited, spreadsheet-based format which will become a part of the MAGE microarray data standard that can be used for annotating and communicating microarray data in a MIAME compliant fashion. MAGE-TAB will enable laboratories without bioinformatics experience or support to manage, exchange and submit well-annotated microarray data in a standard format using a spreadsheet. The MAGE-TAB format is self-contained, and does not require an understanding of MAGE-ML or XML. | microarray, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: MIAME is related to: DDBJ Omics Archive is related to: ArrayExpress is related to: caArray has parent organization: MAGE |
PMID:17087822 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157259, biotools:tab2mage | https://bio.tools/tab2mage | SCR_003222 | 2026-07-28 09:40:38 | 5 | ||||||
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RNAhybrid Resource Report Resource Website 100+ mentions |
RNAhybrid (RRID:SCR_003252) | RNAhybrid | service resource, data analysis service, software resource, production service resource, analysis service resource | Software tool for finding the minimum free energy hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode, i.e., the short sequence is hybridized to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction. | microrna, target prediction, free energy, rna, bio.tools |
is listed by: OMICtools is listed by: 3DVC is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Bielefeld University; North Rhine-Westphalia; Germany |
PMID:15383676 DOI:10.1261/rna.5248604 |
Free, Available for download, Freely available | OMICS_00416, biotools:rnahybrid, nif-0000-31412 | https://bio.tools/rnahybrid, https://sources.debian.org/src/rnahybrid/ | SCR_003252 | 2026-07-28 09:40:45 | 477 | ||||||
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PLANTTFDB Resource Report Resource Website 1000+ mentions |
PLANTTFDB (RRID:SCR_003362) | PlantTFDB | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource | Comprehensive plant transcription factor database. Interface to allow users to search the database by IDs or free texts, to make sequence similarity search against TFs of all or individual species, and to download TF sequences for local analysis.PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors | transcription factor, expression, regulation, interaction, conserved element, phenotype, function, evolution, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Database of Poplar Transcription Factors is related to: Plant Ontology has parent organization: Peking University; Beijing; China |
China 863 ; China 973 ; NSFC ; China NSFC |
PMID:24174544 PMID:17933783 PMID:21097470 |
Free, Available for download, Freely available | nif-0000-03311, biotools:planttfdb_2.0, OMICS_00560, r3d100010137 | https://bio.tools/planttfdb_2.0, https://doi.org/10.17616/R3JG6V | http://planttfdb.cbi.pku.edu.cn | SCR_003362 | , PlantTFDB 2.0, Plant Transcription Factor Database | 2026-07-28 09:40:41 | 1109 | |||
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Weighted Gene Co-expression Network Analysis Resource Report Resource Website 1000+ mentions |
Weighted Gene Co-expression Network Analysis (RRID:SCR_003302) | WGCNA | software application, software resource, data analysis software, data processing software | Software R package for weighted correlation network analysis. WGCNA is also available as point-and-click application. Unfortunately this application is not maintained anymore. It is known to have compatibility problems with R-2.8.x and newer, and the methods it implements are not all state of the art., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, co-expression, analysis, network, bio.tools, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of California at Los Angeles; California; USA |
NCI P50CA092131; NIDA 1R01DA030913-01; NIDCR R01DE019255; NIAID U19 AI063603-01 |
PMID:19114008 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31889, biotools:crosslinkwgcna | http://labs.genetics.ucla.edu/horvath/htdocs/CoexpressionNetwork/Rpackages/WGCNA/#citation, https://bio.tools/crosslinkwgcna | SCR_003302 | WGCNA: an R package for weighted correlation network analysis | 2026-07-28 09:40:41 | 1860 | ||||
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QGene Resource Report Resource Website 100+ mentions |
QGene (RRID:SCR_003209) | QGene | software application, data analysis software, source code, software resource, data processing software, simulation software | A free, open-source, computationally efficient Java program for comparative analyses of QTL mapping data and population simulation that runs on any computer operating system. (entry from Genetic Analysis Software) It is written with a plug-in architecture for ready extensibility. The software accommodates line-cross mating designs consisting of any arbitrary sequence of selfing, backcrossing, intercrossing and haploid-doubling steps that includes map, population, and trait simulators; and is scriptable. Source code is available on request. | gene, genetic, genomic, java, qtl mapping, trait analysis, trait, population, simulation, map, quantitative trait locus, comparison, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Kansas State University; Kansas; USA |
NSF DBI 0109879; USDA-NRI Applied Plant Genomics Program 2004-35317-14867 |
PMID:18940826 | Free, Available for download, Freely available | biotools:qgene, nif-0000-31383 | https://bio.tools/qgene | http://coding.plantpath.ksu.edu/qgene | SCR_003209 | QGene - Software for QTL data exploration | 2026-07-28 09:40:44 | 126 | |||
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Xenbase Resource Report Resource Website 100+ mentions |
Xenbase (RRID:SCR_003280) | XenBase | service resource, data or information resource, data repository, image repository, database, storage service resource | Data collection for Xenopus laevis and Xenopus tropicalis biology and genomics. | molecular neuroanatomy resource, dna target, protein target, gene, genome, function, sequence, orthology, publication, gene expression, model organism, genomics, development, annotation, blast, development stage, publication, in situ hybridization, immunohistochemistry, video resource, organism-related portal, experimental protocol, organism supplier, data analysis service, developmental stage, gold standard, bio.tools, FASEB list, RRID Community Authority |
is listed by: OMICtools is listed by: One Mind Biospecimen Bank Listing is listed by: bio.tools is listed by: Debian is related to: Bgee: dataBase for Gene Expression Evolution has parent organization: University of Calgary; Alberta; Canada is parent organization of: Xenopus Anatomy Ontology |
NICHD R01 HD045776; NICHD P41 HD064556 |
PMID:23125366 PMID:19884130 PMID:36755307 |
Free, Available for download, Freely available | biotools:xenbase, OMICS_01665, nif-0000-01286, r3d100010279 | http://www.xenbase.org/entry/, https://bio.tools/xenbase, https://doi.org/10.17616/R3MP4S | SCR_003280 | Xenbase: Xenopus laevis and tropicalis biology and genomics resource | 2026-07-28 09:40:39 | 446 |
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