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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MetabolExpert Resource Report Resource Website 1+ mentions |
MetabolExpert (RRID:SCR_014908) | software resource | Software tool for initial estimation of the structural formula of metabolites, which might be formed by a substance in humans, animals or in plants. MetabolExpert is also capable of predicting the most common metabolic pathways in animals, exporting results to SDF and RDF format and graphical highlighting that empasizes the essence of metabolic reactions that occurred. | metabolites, metabolism, analysis, chemical, modeling, prediction | Commercial | SCR_014908 | 2026-02-14 02:02:59 | 3 | |||||||||||
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Leadscope Resource Report Resource Website 10+ mentions |
Leadscope (RRID:SCR_014904) | software resource | Commercial developer of database and predictive model software tools used in chemical toxicity assessment. | predictive software, modeling, chemical toxicity, analysis | Commercial | SCR_014904 | 2026-02-14 02:03:03 | 31 | |||||||||||
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Varian Medical Systems, Inc. Resource Report Resource Website 1+ mentions |
Varian Medical Systems, Inc. (RRID:SCR_017372) | commercial organization | Manufacturer located in Palo Alto, California, USA, that has made developments in fields of radiotherapy, radiosurgery, X-ray tube technology, digital image detectors, cargo screening, and non-destructive testing. Varian technology and software for processing diagnostic X-ray images is being used in radiotherapy and analysis. | Manufacturer, commercial, company, component, radiotherapy, spectrometry, software, analysis, therapy, medical, imaging, technology, development | grid.482350.8, ISNI: 0000 0004 0482 3442, Wikidata: Q30343843 | https://ror.org/049tb1q96 | SCR_017372 | Varian | 2026-02-14 02:03:11 | 8 | |||||||||
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Batch Data and Analysis Tool Resource Report Resource Website 1+ mentions |
Batch Data and Analysis Tool (RRID:SCR_017515) | data or information resource, service resource | Software tool to access various mouse genome information in batch format. Batch data and analysis tools. | Mouse, genome, information, batch, format, data, analysis, tool | has parent organization: Mouse Genome Informatics (MGI) | Free, Freely available | SCR_017515 | 2026-02-14 02:03:13 | 3 | ||||||||||
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BioRad Bio-Plex 200 System Resource Report Resource Website 100+ mentions |
BioRad Bio-Plex 200 System (RRID:SCR_018026) | instrument resource | Suspension array system which offers protein and nucleic acid researchers multiplex assay solution permiting analysis of up to 100 biomolecules in single sample. | ABRF, suspension array reader, protein, nucleid acid, assay, analysis, instrument, equipment, Bio-Rad | is listed by: USEDit | https://rai.unam.mx/manuales/umyp_Manual_Bioplex.pdf | SCR_018026 | , Bio-Plex 200 System, Bio-Plex 200 Suspension Array System, BioRad suspension array reader | 2026-02-14 02:03:29 | 151 | |||||||||
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Luminex 100 or 200 Flow Cytometry Analyzer System Resource Report Resource Website 10+ mentions |
Luminex 100 or 200 Flow Cytometry Analyzer System (RRID:SCR_018025) | instrument resource | Flow cytometry analyzer system for individual labs that performs up to 100 different tests in single reaction volume and can use either magnetic beads or plain polystyrene beads. Luminex 200 offers higher sample throughput with 96-well plate read time of only 45 minutes. | ABRF, suspension array analyzer, flow cytometry, magnetic bead, polystyrene bead, analysis, Luminex Corporation, instrument, equipment | is listed by: USEDit | https://pedsresearch.org/uploads/pages/img/LuminexManual_LX100.pdf | SCR_018025 | Luminex 100/200 System | 2026-02-14 02:03:15 | 17 | |||||||||
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HED Tags Resource Report Resource Website 1+ mentions |
HED Tags (RRID:SCR_014074) | HED | data or information resource, narrative resource, standard specification | Strategy guide for HED Annotation. Framework for systematically describing laboratory and real world events.HED tags are comma separated path strings. Organized in forest of groups with roots Event, Item, Sensory presentation, Attribute, Action, Participant, Experiment context, and Paradigm. Used for preparing brain imaging data for automated analysis and meta analysis. Applied to brain imaging EEG, MEG, fNIRS, multimodal mobile brain or body imaging, ECG, EMG, GSR, or behavioral data. Part of Brain Imaging Data Structure standard for brain imaging. | Data, structure, standard, EEG, brain, imaging, comma, separated, path, string, analysis, MEG, fNIRS, multimodal, ECG, EMG, GSR, behavioral, BRAIN Initiative |
is used by: NIMH Data Archive is used by: HeadIT is used by: OpenNeuro is recommended by: BRAIN Initiative has parent organization: University of California at San Diego; California; USA |
Swartz Foundation ; Army Research Laboratory Cooperative Agreement ; NIMH R01MH084819; NINDS R01 NS047293 |
PMID:27799907 | Free, Freely available | SCR_017630 | SCR_014074 | Hierarchical Event Descriptor Tags, Hierarchical Event Descriptor, HED, HED tags | 2026-02-14 02:02:56 | 7 | |||||
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nanoPOTS Resource Report Resource Website 1+ mentions |
nanoPOTS (RRID:SCR_017129) | instrument resource | Nanodroplet processing platform for deep and quantitative proteome profiling of 10 to 100 mammalian cells. It enhances efficiency and recovery of sample processing by downscaling processing volumes. | nanodroplet, processing, platform, quantitative, proteome, profiling, analysis, mammalian, cell, small, volume | has parent organization: Pacific Northwest National Laboratory | NIBIB R21 EB020976; NCI R33 CA225248; NIGMS P41 GM103493; NIDDK UC4 DK104167; NIDDK DP3 DK110844; NIH Office Of The Director S10 OD016350; JDRF |
PMID:29491378 | SCR_017129 | 2026-02-14 02:03:08 | 1 | |||||||||
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ZetaView Nanoparticle Tracking Analyzer Resource Report Resource Website 100+ mentions |
ZetaView Nanoparticle Tracking Analyzer (RRID:SCR_016647) | ZetaView NTA | instrument resource | Instrument for nanoparticle tracking analysis. A semi-automated method for the characterization of extracellular vesicles with associated analysis software by ParticleMetrix GmbH. | instrument, nanoparticle, tracking, analysis, ParticleMetrix GmbH, extracellular, vesicles, method | Commercially available | https://partoshar.com/administrator/files/UploadFile/DLS/Zeta-View/Catalog/zetaview-en.pdf | SCR_016647 | ZetaView NTA, ZetaView Nanoparticle Tracking Analyzer | 2026-02-14 02:03:18 | 290 | ||||||||
|
CHAoS Resource Report Resource Website 10+ mentions |
CHAoS (RRID:SCR_005174) | CHAoS | software resource | A Perl-based system for annotation of variants identified in high-throughput sequencing experiments. Functionality includes annotation of variants with information relating to population genetics, known transcripts, positional records, and sequence motif-based prediction. In addition, annotated variants can be summarized and extracted to facilitate downstream analysis. There is also basic support for gene-based biological annotation, and eventually will include tools for variant and genotype analysis and visualization. | annotation, analysis, visualization, variant, high-throughput sequencing, perl, population genetic, transcript, positional record, sequence, motif, genotype |
is listed by: OMICtools has parent organization: Wellcome Trust Centre for Human Genetics |
GNU General Public License, v2 | OMICS_00170 | SCR_005174 | chaos - Annotation analysis and visualization of variants from high-throughput sequencing experiments | 2026-02-14 02:00:50 | 26 | |||||||
|
HIVCD Resource Report Resource Website |
HIVCD (RRID:SCR_005201) | HIVCD | software resource | Informatics software tool to identify patient sequences that are too similar to happen by chance alone. Highly similar sequences are likely to occur from contamination or other situations like geographic linkage. | java, perl, contamination, sequencing, error, pairwise comparison, testing, analysis, contamination screening |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23583427 | Apache License, v2 | OMICS_00220 | SCR_005201 | HIVCD - Informatics tool for contamination screening in the HIV sequencing lab, HIV Contamination Detection | 2026-02-14 02:00:50 | 0 | ||||||
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ChIPMonk Resource Report Resource Website 1+ mentions |
ChIPMonk (RRID:SCR_002975) | ChIPMonk | software resource | Software tool to visualize and analyse ChIP-on-chip array data. Main features: * Import of data from Nimblegen arrays (other formats can be added if people send us examples) * Normalization of data (both per array and per probe) * Various data plotting options to assess data quality and the effectiveness of normalization * Creation of data groups for visualization and analysis * Visualization of data against an annotated genome. * Statistical analysis of data to find probes of interest * Creation of reports containing probes, data and genome annotation Note: This project is no longer being developed, but critical bug fixes will still be provided | java, chip, chip-on-chip, plotting, normalization, visualization, genome, annotation, probe, array, analysis |
is listed by: OMICtools has parent organization: Babraham Institute |
Free, Available for download, Freely available | OMICS_02043, nif-0000-30159 | http://www.bioinformatics.bbsrc.ac.uk/projects/chipmonk/ | SCR_002975 | 2026-02-14 02:00:21 | 4 | |||||||
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SciRoKo Resource Report Resource Website 1+ mentions |
SciRoKo (RRID:SCR_000941) | software resource | Comparative genomics software that assists in whole genome microsatellite search and investigation. The command line version is called SciRoKoCo. The perl script DesignPrimer can be used to design PCR primer pairs for the SciRoKo output. | genomics, comparative, genome, microsatellite, analysis, investigation | is listed by: OMICtools | PMID:17463017 | Free, Available for download, Freely available | OMICS_00113 | SCR_000941 | 2026-02-14 01:59:50 | 6 | ||||||||
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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 | 2026-02-14 01:59:38 | 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 | 2026-02-14 01:59:39 | 5 | |||||||
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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 | 2026-02-14 01:59:42 | 2 | ||||||
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TOPPAS Resource Report Resource Website 1+ mentions |
TOPPAS (RRID:SCR_000533) | software resource | A graphical user interface (GUI) for rapid composition of HPLC-MS analysis workflows. Workflow construction is reduced to drag-and-drop of analysis tools and adding connections in between. | gui, graphical user interface, analysis, hplc-ms, workflow |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22583024 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02640 | http://open-ms.sourceforge.net/workflow-integration/toppasworkflows/ | SCR_000533 | The OpenMS Proteomics Pipeline Assistant, TOPP Pipeline Assistant | 2026-02-14 01:59:46 | 1 | ||||||
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MetaDrug Resource Report Resource Website 1+ mentions |
MetaDrug (RRID:SCR_000461) | MetaDrug | commercial organization | A leading systems pharmacology solution that incorporates extensive manually curated information on biological effects of small molecule compounds. Predictive and analytical algorithms look at chemical compounds from different angles in one integrated workflow are available for: * Individual previously described compounds to look up their known information and predict currently unknown properties * Individual newly synthesized or isolated compounds to predict their properties from its structures * Compound libraries to extract known and predict new properties of individual compounds and perform their comparison and prioritization | pharmacology, compound, pathway, target, metabolite, prediction, toxicity, indication, metabolism, gene, protein, analysis, drug effect | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01584 | SCR_000461 | 2026-02-14 01:59:43 | 1 | ||||||||
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Mini Analysis Guide for Microarrays Resource Report Resource Website 1+ mentions |
Mini Analysis Guide for Microarrays (RRID:SCR_000596) | MAGMA | data or information resource, experimental protocol, narrative resource | A collection of cook-book like manuals for various microarray designs. MAGMA is a collaboration between the Norwegian Microarray Consortium NMC and MolMine AS | microarray design, microarray, manual, guide, array, analysis, j-express, import, data processing, global analysis, differential expression, gene set, co-expressed gene |
is listed by: OMICtools has parent organization: J-Express |
OMICS_00772 | SCR_000596 | 2026-02-14 01:59:47 | 3 | |||||||||
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SOAPfusion Resource Report Resource Website 1+ mentions |
SOAPfusion (RRID:SCR_000079) | SOAPfusion | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 22,2022. An open source software tool for fusion discovery with paired-end RNA-Seq reads. The tool follows a different strategy by finding fusions directly and verifying them, differentiating it from all other existing tools by finding the candidate regions and searching for the fusions afterwards. | software, open source, free, RNA, sequencing, data, computing, research, analysis, rna-seq, candidate regions, bio.tools |
is listed by: OMICtools is listed by: SOAP is listed by: bio.tools is listed by: Debian |
Guangdong Innovative Research Team Program ; General Research Fund of the Hong Kong Government |
PMID:24123671 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01358, biotools:soapfusion | https://bio.tools/soapfusion | SCR_000079 | 2026-02-14 01:59:36 | 3 |
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