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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GenNav Resource Report Resource Website 1+ mentions |
GenNav (RRID:SCR_000147) | GenNav | data access protocol, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. GenNav searches GO terms and annotated gene products, and provides a graphical display of a term's position in the GO DAG. | image, gene, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: National Library of Medicine |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149123 | SCR_000147 | 2026-08-15 11:21:41 | 1 | ||||||||
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F2DockClient Resource Report Resource Website 1+ mentions |
F2DockClient (RRID:SCR_000185) | F2DockClient | software resource | A collection of user interfaces packaged into TexMol that allows a user to interactively submit protein-protein docking jobs to a remote computing cluster, monitor the status of the jobs and retrieve and visually display/compare the results. | user interface, protein-protein docking, computing cluster, analysis, | is listed by: OMICtools | National Science Foundation ; National Institutes of Health |
PMID:23483883 | Free, Available for download, Freely available | OMICS_01599 | SCR_000185 | 2026-08-15 11:21:41 | 1 | ||||||
|
FlexX Resource Report Resource Website 1+ mentions |
FlexX (RRID:SCR_000186) | FlexX | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software with two main applications: predicting the binding mode of three-dimensional proteins and virtual high-throughput screening (vHTS) which allows screening of compounds at rapid speeds. | protein binding, analysis, ligand, prediction, compounds, screening, protein-ligand docking, | is listed by: OMICtools | PMID:15382244 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01600 | SCR_000186 | 2026-08-15 11:21:41 | 5 | |||||||
|
Miller Lab at the Penn State Center for Comparative Genomics and Bioinformatics Resource Report Resource Website 1+ mentions |
Miller Lab at the Penn State Center for Comparative Genomics and Bioinformatics (RRID:SCR_000222) | organization portal, data or information resource, laboratory portal, portal | A portal for the Miller Lab at Penn State that does research in comparative genomics and bioinformatics. The website has resources such as web-based applications for genetic databases, software for genomic analysis and publications from the lab. | comparative, genomics, bioinformatics, software, web-based application |
has parent organization: Pennsylvania State University is parent organization of: LASTZ |
nif-0000-30237 | SCR_000222 | 2026-08-15 11:21:42 | 1 | ||||||||||
|
CRASH Resource Report Resource Website 1+ mentions |
CRASH (RRID:SCR_000221) | topical portal, data or information resource, portal | Portal for placebo controlled trial of the effects of 48-hour infusion of corticosteroids on death and on neurological disability, among adults with head injury and some impairment of consciousness. The outcomes will be measured by rates of death and neurological disability. Patients are recruited (or entered by their doctors when informed consent is not obtainable due to impaired cognitive functioning) on a case-by-case basis as head injured patients come through emergency departments. Randomization is done via a 24-hour telephone line that will denote which pack of medication (either the corticosteroids or saline solution as control) to give. | corticosteroid, neurological disability, death, head injury, consciousness, randomized controlled trial, coma, clinical trial, | PMID:15936423 | Public | nif-0000-30274 | SCR_000221 | 2026-08-15 11:21:41 | 4 | |||||||||
|
EnvO Resource Report Resource Website 10+ mentions |
EnvO (RRID:SCR_000182) | EnvO | ontology, data or information resource, controlled vocabulary | Community ontology for the concise, controlled description of environmental features and habitats. It provides a structured vocabulary that is designed to support the annotation of any organism or biological sample with environment descriptors. EnvO contains terms for biomes, environmental features, and environmental material. | biome, environmental feature, environmental material, environment, habitat |
is listed by: BioPortal is related to: Gramene |
The community can contribute to this resource | nlx_153832 | SCR_000182 | Environment Ontology | 2026-08-15 11:21:41 | 20 | |||||||
|
RNAcontext Resource Report Resource Website 1+ mentions |
RNAcontext (RRID:SCR_000179) | RNAcontext | production service resource, web service, data access protocol, software resource, service resource, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Motif finding software suited for using large-scale RNA-binding affinity datasets to determine the relative binding preferences of RNA-binding proteins (RBPs) for a wide range of RNA sequences and structures. The tool is also implemented in a website. | rna-binding protein, motif, rna sequence, rna structure, rna, binding preference, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Toronto; Ontario; Canada |
PMID:20617199 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02253, biotools:rnacontext | https://bio.tools/rnacontext | SCR_000179 | 2026-08-15 11:21:41 | 2 | ||||||
|
Mississippi State University; Mississippi; USA Resource Report Resource Website 1+ mentions |
Mississippi State University; Mississippi; USA (RRID:SCR_000361) | university | Public university in Mississippi with land, sea and space grants that offers degree programs in areas such as agriculture and applied sciences at the undergraduate and graduate levels. | mississippi, land, sea, space, grant, agriculture, applied science |
is parent organization of: Chicken Gene Nomenclature Consortium is parent organization of: AgBase is parent organization of: Bovine Gene Atlas is parent organization of: Corn Fungal Resistance Associated Sequences Database is parent organization of: Bird Base is parent organization of: Mississippi State University Institute for Imaging and Analytical Technologies I2AT Core Facility |
Wikidata Q1939211, GRID grid.260120.7, nlx_23152, ISNI 0000 0001 0816 8287, Crossref Funder ID 100007250 | https://ror.org/0432jq872 | SCR_000361 | 2026-08-15 11:21:48 | 1 | |||||||||
|
TAPS Resource Report Resource Website 1+ mentions |
TAPS (RRID:SCR_000356) | software resource | A bioinformatic tool for the identification of allele-specific copy numbers in tumor samples using data from Affymetrix SNP arrays. | standalone software, affymetrix |
is listed by: OMICtools has parent organization: Google Code |
PMID:22023820 | OMICS_02571 | SCR_000356 | Tumor Aberration Prediction Suite | 2026-08-15 11:21:43 | 2 | ||||||||
|
University of Sydney; Sydney; Australia Resource Report Resource Website 1+ mentions |
University of Sydney; Sydney; Australia (RRID:SCR_000381) | university | A public research university in Sydney, Australia that offers a wide range of degree programs at the undergraduate and graduate level. | public, research, university, sydney, australia, training service resource |
uses: LabArchives is related to: International AMD Genetics Consortium is related to: LabArchives is parent organization of: Using our Brains Tissue Donor Program is parent organization of: Australian New Zealand Clinical Trials Registry is parent organization of: MF-GE is parent organization of: OMIA - Online Mendelian Inheritance in Animals is parent organization of: Australian Microscopy and Microanalysis Research Facility is parent organization of: CiteFuse |
ISNI:0000 0004 1936 834X, nlx_143763, grid.1013.3, Crossref funder ID:501100001774, Wikidata:Q487556 | https://ror.org/0384j8v12 | SCR_000381 | University of Sydney | 2026-08-15 11:21:49 | 1 | ||||||||
|
is-rSNP Resource Report Resource Website 1+ mentions |
is-rSNP (RRID:SCR_000387) | is-rSNP | software resource | Software tool that predicts whether a single nucleotide polymorphism (SNP) is a regulatory SNP (rSNP). For a given SNP, and using a statistical framework, it can successfully predict the set of transcription factors (TFs) for which binding is affected. The algorithm provides the statistical power to scan large numbers of SNPs, making it suitable to use to screen all associated SNPs output by a typical genome-wide association studies (GWAS). | genome-wide association study, single nucleotide polymorphism, transcription factor, regulatory single nucleotide polymorphism, in silico |
is listed by: OMICtools has parent organization: University of Melbourne; Victoria; Australia |
PMID:20823317 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01930 | SCR_000387 | In silico regulatory SNP detection, is-rSNP: in silico regulatory SNP detection | 2026-08-15 11:21:44 | 1 | ||||||
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AS-Peak Resource Report Resource Website 1+ mentions |
AS-Peak (RRID:SCR_000380) | ASPeak | software resource | A software that utilizes a peak detection algorithm to identify RNA-protein binding sites. | rna, peak detection, protein, binding, site, algorithm, analysis |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23929032 | Free, Available for download, Freely available | OMICS_00566 | https://omictools.com/aspeak-tool | SCR_000380 | 2026-08-15 11:21:44 | 2 | ||||||
|
GENSENG Resource Report Resource Website 1+ mentions |
GENSENG (RRID:SCR_000378) | data processing software, software application, data analysis software, software resource | Software for detecting copy number variations from next generation sequencing data. Used to identify regions of discrete copy number changes while simultaneously accounting for effects of multiple confounders. | next generation sequencing data, detecting copy number variations, discrete copy number changes, identify regions |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23275535 | Free, Available for download, Freely available | OMICS_00345 | SCR_000378 | 2026-08-15 11:21:49 | 1 | ||||||||
|
flowFlowJo Resource Report Resource Website 10+ mentions |
flowFlowJo (RRID:SCR_000410) | software resource | A Bioconductor package that can import gates defined by the commercial package FlowJo and work with them in a manner consistent with the other flow packages in Bioconductor. FlowJo is a commercial GUI based software package from TreeStar Inc. for the visualization and analysis of flow cytometry data. One of the FlowJo standard export file types is the FlowJo Workspace. This is an XML document that describes files and manipulations that have been performed in the FlowJo GUI environment. This package can take apart the FlowJo workspace and deliver the data into R in the flowCore paradigm. | software package, mac os x, unix/linux, windows, r, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:19956421 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05598 | SCR_000410 | flowFlowJo - Tools for extracting information from a FlowJo workspace and working with the data in the flowCore paradigm | 2026-08-15 11:21:50 | 21 | |||||||
|
University of Texas at Dallas; Texas; USA Resource Report Resource Website 1+ mentions |
University of Texas at Dallas; Texas; USA (RRID:SCR_000375) | UTD | university | A public research university in Texas that offers degree programs in engineering, business, political science and the natural sciences at the undergraduate and graduate levels. The university also houses research that focuses on space science, bioengineering, cybersecurity, nanotechnology, and behavioral and brain sciences. | public, research, engineering, political science, natural science, business, space science, bioengineering, cybersecurity, nanotechnology, behavioral, brain sciences, neuroscience, psychology |
has parent organization: University of Texas System; Texas; USA is parent organization of: DOMINE: Database of Protein Interactions is parent organization of: University of Texas at Dallas School of Behavioral and Brain Sciences is parent organization of: ExPosition Packages is parent organization of: MB-GAN is parent organization of: University of Texas at Dallas UTD Genome Center Core Facility is parent organization of: University of Texas at Dallas UTD Imaging and Histology Core Facility |
grid.267323.1, nlx_11355, ISNI:0000 0001 2151 7939, Wikidata:Q1781394 | https://ror.org/049emcs32 | SCR_000375 | 2026-08-15 11:21:49 | 1 | ||||||||
|
BD Biosciences: FACSCalibur Flow Cytometry System Resource Report Resource Website 100+ mentions |
BD Biosciences: FACSCalibur Flow Cytometry System (RRID:SCR_000401) | BD FACSCalibur system | instrument resource | Automated benchtop flow cytometry system. It allows measuring four fluorochrome-conjugates, forward and side scatter., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | flow cytometry, hardware, instrument, equipment | has parent organization: BD Biosciences | THIS RESOURCE IS NO LONGER IN SERVICE | https://drive.google.com/file/d/1v6yeGl7IxHS0_Ezn35dZ9qzu27jIBh52/view?usp=drivesdk | SciRes_000153 | https://www.bdbiosciences.com/content/dam/bdb/marketing-documents/BD_FACSCalibur_instructions.pdf | SCR_000401 | FACSCalibur flow cytometer | 2026-08-15 11:21:44 | 411 | |||||
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Opal Research Resource Report Resource Website 1+ mentions |
Opal Research (RRID:SCR_000405) | data processing software, software application, data analysis software, software resource, sequence analysis software | Software which integrates a comprehensive, automated genome annotation engine with the VAAST and Phevor disease gene prioritization tools to rank gene variants on the severity of their impact on protein function and likelihood to cause disease. Each variant in a gene is analyzed for its impact on protein function, conservation and frequency. Each gene is ranked rather than filtered in order to ensure critical targets are not prematurely removed. | sequence analysis software, genome interpretation, variant prioritization, disease gene prioritization, next-generation sequencing, clinical interpretation, clinical genomics software, genome, protein function, disease, genomic variant, mutation | is related to: VAAST | PMID:23895124 | Restricted | SciRes_000140 | SCR_000405 | Omicia Opal Research, Omicia Opal, Opal Research Variant Interpretation | 2026-08-15 11:21:50 | 1 | |||||||
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Lasergene's SeqMan Pro Resource Report Resource Website 1+ mentions |
Lasergene's SeqMan Pro (RRID:SCR_000283) | data processing software, software application, data analysis software, software resource, data visualization software | Software for analysis and DNA sequence assembly of Sanger data. It also provides visualizations and analysis of next-gen projects assembled by SeqMan NGen. | dna, sequence, analysis, sanger, snp discovery, data visualization |
is listed by: OMICtools works with: GenVision |
Restricted | OMICS_01810 | SCR_000283 | Lasergenes SeqMan Pro, SeqMan Pro, SeqMan Pro - Software for Contig Assembly and Analysis Including SNP Discovery Coverage Evaluation and Project Annotation, DANSEUR Lasergenes SeqMan Pro | 2026-08-15 11:21:42 | 5 | ||||||||
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IrfanView Resource Report Resource Website 10+ mentions |
IrfanView (RRID:SCR_000315) | software resource | An open source graphic viewer. Some features include batch conversion, paint options, basic editing and several supported file formats. It is compatible with Windows 9x, ME, NT, 2000, XP, 2003 , 2008, Vista, Windows 7, Windows 8, and Windows 10. | graphic viewer, open source, windows | Free, Available for download, Freely available | nlx_157659 | SCR_000315 | 2026-08-15 11:21:43 | 13 | ||||||||||
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flowStats Resource Report Resource Website 1+ mentions |
flowStats (RRID:SCR_000399) | software resource | Software using statistical methods and functionality to analyze flow data that is beyond the basic infrastructure provided by the flowCore package. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_05611 | SCR_000399 | flowStats - Statistical methods for the analysis of flow cytometry data | 2026-08-15 11:21:44 | 1 |
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