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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GCE Resource Report Resource Website 10+ mentions |
GCE (RRID:SCR_017332) | data analysis software, data processing software, software application, software resource | Software tool for estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects. Used as general and assembly independent method for estimating genomic characteristics. | estimation, genomic, characteristic, analysis, k-mer, frequencey, de novo | ftp://ftp.genomics.org.cn/pub/gce | SCR_017332 | Genomic Characteristics Estimation | 2026-09-05 06:28:22 | 15 | ||||||||||
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MRspa Resource Report Resource Website 10+ mentions |
MRspa (RRID:SCR_017292) | data analysis software, data processing software, software application, software resource | Software package to post process MR spectroscopy data. Magnetic Resonance signal processing and analysis software. Runs under Matlab. | post, process, magnetic, resonance, spectroscopy, data, analysis |
has parent organization: University of Minnesota Twin Cities; Minnesota; USA works with: MATLAB |
Restricted | SCR_017292 | Magnetic Resonance signal processing and analysis | 2026-09-05 06:28:22 | 19 | |||||||||
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IKAP Resource Report Resource Website 1+ mentions |
IKAP (RRID:SCR_017417) | data analysis software, data processing software, software application, software resource | Software tool for identifying K mAjor cell population groups in single-cell RNA-seq analysis. Algorithm identifying major cell groups that improves differentiating by tuning parameters for clustering. Using multiple datasets improves identification of major cell types and facilitates cell ontology curation. | Identify, cell, population, group, single, cell, RNAseq, analysis, clustering, dataset | DOI:10.1101/596817 | Free, Available for download, Freely available | SCR_017417 | Identifying K mAjor cell Population | 2026-09-05 06:28:24 | 2 | |||||||||
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Glimma Resource Report Resource Website 10+ mentions |
Glimma (RRID:SCR_017389) | data analysis software, data processing software, data visualization software, software application, software resource | Software package for interactive graphics for gene expression analysis. Generates interactive visualisations for analysis of RNA-sequencing data. | Interactive, graphic, gene, expression, analysis, visualisation, RNAseq, data |
uses: LIMMA uses: edgeR uses: DESeq2 |
NHMRC ; Victorian State Government Operational Infrastructure Support and Australian Government ; Viertel Fellowship |
PMID:28203714 | Free, Available for download, Freely available | SCR_017389 | 2026-09-05 06:28:23 | 23 | ||||||||
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The Decoding Toolbox Resource Report Resource Website 10+ mentions |
The Decoding Toolbox (RRID:SCR_017424) | TDT | data analysis software, data processing software, software application, software resource | Software Matlab toolbox for multivariate analysis of functional and structural MRI data. Software package for multivariate analyses of functional imaging data. | Multivariate, analysis, structural, MRI, data, functional, imaging, brain | German Ministry of Education and Research ; German Research Foundation |
PMID:25610393 | Free, Available for download, Freely available | SCR_017424 | 2026-09-05 06:28:24 | 16 | ||||||||
|
BEAST2 Resource Report Resource Website 100+ mentions |
BEAST2 (RRID:SCR_017307) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software package for advanced Bayesian evolutionary analysis by sampling trees. Used for phylogenetics, population genetics and phylodynamics. Program for Bayesian phylogenetic analysis of molecular sequences. Estimates rooted, time measured phylogenies using strict or relaxed molecular clock models. Framework can be extended by third parties. Comprised of standalone programs including BEAUti, BEAST, MASTER, RBS, SNAPP, MultiTypeTree, BDSKY, LogAnalyser, LogCombiner, TreeAnnotator, DensiTree and package manager. | Bayesian, evolutionary, sampling, tree, phylogenic, analysis, Markov, chain, monte carlo, phylogenetic, population, genetic, phylodynamic, sequence |
is related to: BASTA is related to: BEAST is related to: PhyDyn has parent organization: University of Auckland; Auckland; New Zealand |
EMBL ; European Research Council ; Max Planck Society ; NIGMS U01 GM110749; Royal Society of New Zealand Marsden award ; Swiss National Science foundation |
PMID:30958812 | Free, Available for download, Freely available | SCR_017307 | , Beast 2.5 | 2026-09-05 06:28:22 | 211 | |||||||
|
SequelQC Resource Report Resource Website 1+ mentions |
SequelQC (RRID:SCR_017279) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool that calculates key statistics and generates publication quality plots for raw PacBio Sequel data. Open source software for analyzing PacBio Sequel raw sequence data. | raw, data, PacBio, Sequel, analysis, sequence, DNA, read, length, plot | NSF Plant Genome Research Program IOS-1744001 | DOI:10.1101/611814 | Free, Freely available, Available for download | SCR_017279 | 2026-09-05 06:28:21 | 2 | |||||||||
|
QtiPlot Resource Report Resource Website 10+ mentions |
QtiPlot (RRID:SCR_017311) | data analysis software, data processing software, software application, software resource | Software tool for data analysis and scientific visualization by IONDEV SRL. | data, analysis, visualization, IONDEV SRL | Restricted | SCR_017311 | 2026-09-05 06:28:22 | 30 | |||||||||||
|
Cancer Dependency Map Portal Resource Report Resource Website 1000+ mentions |
Cancer Dependency Map Portal (RRID:SCR_017655) | DepMap Portal | catalog, data or information resource, data set, database, portal, project portal | Portal for identifying genetic and pharmacologic dependencies and biomarkers that predicts them by providing access to datasets, visualizations, and analysis tools that are being used by Cancer Dependency Map Project at Broad Institute. Project to systematically identify genes and small molecule dependencies and to determine markers that predict sensitivity. All data generated by DepMap Project are available to public under CC BY 4.0 license on quarterly basis and pre-publication. | Cancer, vulnerability, dataset, visualization, analysis, tool, catalog, biomarker, genetic, drug, sensitivity, tumor, model, FASEB list | has parent organization: Broad Institute | Free, Available for download, Freely available | SCR_017655 | Dependency Map Portal, Dependency Map portal, Cancer DepMap, Cancer Dependency Map Project | 2026-09-05 06:28:27 | 1417 | ||||||||
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Deep Blue Epigenomic Data Server Resource Report Resource Website 1+ mentions |
Deep Blue Epigenomic Data Server (RRID:SCR_017490) | access service resource, data access protocol, data or information resource, service resource, software resource, web service | Central data access hub for large collections of epigenomic data. It organizes data from different sources using controlled vocabularies and ontologies. Data Server for storing, organizing, searching, and retrieving genomic and epigenomic data, handling associated metadata, and to perform different types of analysis. | Data, epigenomic, collection, ontology, storing, distributing, organizing, retriving, searching, genetic, metadata, analysis |
uses: ENCODE uses: Blueprint Epigenome uses: NIH Roadmap is related to: Roadmap Epigenomics Project |
EU ; German Science Ministry |
Free, Freely available | SCR_017490 | 2026-09-05 06:28:25 | 2 | |||||||||
|
iBright Analysis Software Resource Report Resource Website 10+ mentions |
iBright Analysis Software (RRID:SCR_017632) | data analysis software, data processing software, image analysis software, software application, software resource | Software for organizing and analyzing blot and gel images captured on iBright Imaging Systems. Available as desktop version PC and Mac OS compatible and cloud-based version accessible via web browser through Connect platform. | Invitrogen, image, adjustment, data, analysis, blot, gel, iBright Imaging System | Free, Available for download, Freely available | SCR_017632 | 2026-09-05 06:28:27 | 21 | |||||||||||
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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 | 2026-09-05 06:28:25 | 3 | ||||||||||
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RAMPAGE Resource Report Resource Website 100+ mentions |
RAMPAGE (RRID:SCR_017590) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2021.Web based structural analysis tool for any uploaded PDB file, producing Ramachandran plots, computing dihedral angles and extracting sequence from PDB. Used to visualize dihedral angles ψ against φ of amino acid residues in protein structure. | Ramachandran, plot, analysis, upload, PDB, file, coputing, dihedral, angle, extracting, sequence, protein, amino acid, residue, structure | has parent organization: University of Cambridge; Cambridge; United Kingdom | THIS RESOURCE IS NO LONGER IN SERVICE. | SCR_017590 | 2026-09-05 06:28:26 | 136 | ||||||||||
|
JWatcher Resource Report Resource Website 50+ mentions |
JWatcher (RRID:SCR_017595) | data acquisition software, data analysis software, data analytics software, data processing software, software application, software resource | Software Java tool for quantitative analysis of behavior. Used to address any theoretical problem that requires complex sequence of actions to be scored by human observer. Runs on microcomputer providing Java Virtual Machine[TM] and has been tested on Windows[TM] and Macintosh[TM] systems. Legacy version (version 0.9) works on older systems (Macintosh OS-9 and Windows-98), while Version 1.0 works well on Macintosh OS-X and Windows XP systems. JWatcher Video works best on Windows XP systems and has reduced functionality running in Macintosh OS-X. JWatcher-Palm can be used to acquire data on Palm OS[TM] equipped device and analyze it on your main computer. | Quantitative, analysis, behavior, theoretical, problem, action, scored, human, observer |
has parent organization: University of California at Los Angeles; California; USA has parent organization: Macquarie University; Sydney; Australia |
Australian Research Council ; Macquarie University ; NIMH R21 MH065226 |
Free, Available for download, Freely available | SCR_017595 | 2026-09-05 06:28:26 | 53 | |||||||||
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TIGS Resource Report Resource Website 1+ mentions |
TIGS (RRID:SCR_017565) | data or information resource, data repository, narrative resource, service resource, storage service resource, training material, workflow | Repository to share analysis procedure, data and help readers or reviewers to know more detail of this work, reproduce or make use of results they are interested in. | Share, analysis, procedure, data, tumor, immunogenicity | Free, Available for download, Freely available | SCR_017565 | Tumor Immunogenicity Score | 2026-09-05 06:28:25 | 1 | ||||||||||
|
ChemRICH Resource Report Resource Website 10+ mentions |
ChemRICH (RRID:SCR_017609) | analysis service resource, production service resource, service resource, software resource, web application | Software tool for chemical similarity enrichment analysis of metabolomics datasets. Used in studies to uncover biological mechanisms in organisms under genetic or environmental stress in system biology manner or finding risk factors for chronic diseases in exposome wise association studies using blood specimens. Allows users to realize pathway analysis. | Chemical, similarity, enrichment, analysis, metabolomic, dataset, genetic, environmental, stress, risk, factor, chronic, disease, exposome, association, blood, speciment |
is listed by: OMICtools has parent organization: University of California at Davis; California; USA |
PMID:29109515 | Free, Freely available | https://github.com/barupal/chemrich | SCR_017609 | 2026-09-05 06:28:26 | 26 | ||||||||
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vbSPT Resource Report Resource Website 1+ mentions |
vbSPT (RRID:SCR_017554) | data analysis software, data processing software, software application, software resource | Software package for analysis of single particle diffusion trajectories, where diffusion constants switch randomly according to Markov process. Analytical tool to combine information from thousands of short single-molecule trajectories of intracellularly diffusing proteins. Has ability to learn number of diffusive states directly from data, in addition to model parameters such as transition rates and diffusion constants. | Analysis, single, particle, diffusion, trajectory, Markov, short, molecule, intracellularly, protein, data, transition, state | PMID:23396281 | Free, Available for download, Freely available | https://sourceforge.net/projects/vbspt/files/latest/download?source=files | SCR_017554 | variational Bayes single particle tracking | 2026-09-05 06:28:25 | 3 | ||||||||
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Rotor-Gene 6000 series software Resource Report Resource Website 1+ mentions |
Rotor-Gene 6000 series software (RRID:SCR_017552) | data analysis software, data processing software, software application, software resource | Rotor-Gene real-time analysis software system for ROTOR GENE 6000 REAL-TIME PCR machine. Software has been refined to provide an intuitive, Wizard driven interface, enabling flexibility and automation. Build-in extensive analysis, graphing and statistical functions. Unlimited use software license for Windows XP, Pentium IV (2GHz) or higher PC. | Rotor, Gene, 6000 Real Time, PCR machine, analysis, graphing, statistical, function | Free, Available for download, Freely available | https://www.baylor.edu/content/services/document.php/187886.pd | SCR_017552 | Rotor-Gene 6000 series software 1.7 | 2026-09-05 06:28:25 | 3 | |||||||||
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LabChart Reader Resource Report Resource Website 100+ mentions |
LabChart Reader (RRID:SCR_017551) | data analysis software, data processing software, software application, software resource | LabChart data analysis software creates a platform for all of your recording devices to work together, allowing you to acquire biological signals from multiple sources simultaneously and apply advanced calculations and plots as your experiment unfolds. LabChart Reader is free version of software that allows to analyse with some limitations. LabChart Reader doesn’t allow saving of data - export image only. Has data pad for analysis. | Adinstruments, LabChart, data, analysis, calculation, plot | is related to: LabChart | https://www.adinstruments.com/products/labchart/versions-and-licenses | SCR_017551 | LabChart Reader software 8.1, LabChart Reader software | 2026-09-05 06:28:25 | 144 | |||||||||
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OmniPlex Software Resource Report Resource Website 10+ mentions |
OmniPlex Software (RRID:SCR_014803) | data acquisition software, data processing software, data visualization software, software application, software resource | Neural data acquisition software for signal visualization in neuron recordings along with spike wave-form classification methods. It is made up of the PlexControl software program and the OmniPlex Server. | software, neural, neuron data, analysis, pca, data acquisition, signal visualization | Commercially available | SCR_014803 | 2026-09-05 06:27:51 | 26 |
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