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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SCÅTTER Resource Report Resource Website 50+ mentions |
SCÅTTER (RRID:SCR_017271) | web service, data access protocol, analysis service resource, software resource, production service resource, service resource | Software JAVA based application for basic analysis of Small Angle X-ray Scattering datasets. | analysis, data, dataset, small, angle, X ray, scattering, SAXS, BIOISIS | Department of Energy Office of Science Integrated Diffraction Analysis Technologies ; National Cancer Institute Structural Cell Biology of DNA Repair Machines ; National Institute of General Medical Sciences project MINOS |
Restricted | https://bl1231.als.lbl.gov/scatter/ | SCR_017271 | 2026-02-16 09:49:12 | 84 | |||||||||
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Cancer Dependency Map Portal Resource Report Resource Website 1000+ mentions |
Cancer Dependency Map Portal (RRID:SCR_017655) | DepMap Portal | data set, project portal, database, catalog, portal, data or information resource | 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 | 2026-02-16 09:49:17 | 1000 | ||||||||
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iBright Analysis Software Resource Report Resource Website 10+ mentions |
iBright Analysis Software (RRID:SCR_017632) | software application, data processing software, data analysis software, image analysis software, 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 | 2026-02-16 09:49:17 | 17 | |||||||||||
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Batch Data and Analysis Tool Resource Report Resource Website 1+ mentions |
Batch Data and Analysis Tool (RRID:SCR_017515) | service resource, data or information 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 | 2026-02-16 09:49:15 | 3 | ||||||||||
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VG Studio MAX Resource Report Resource Website 10+ mentions |
VG Studio MAX (RRID:SCR_017997) | software application, data processing software, data visualization software, data analysis software, software resource | Software tool for analysis and processing of µCT data, e.g. compiling virtual 3D models of morphological structures in site by Volume Graphics GmbH. Used for visualization of CT data. | Computed tomography, CT, data, analysis, processing, 3D, visualization, CT data | Restricted | SCR_017997 | VGStudio MAX, VG Studio MAX 3.1, VGStudio | 2026-02-16 09:49:22 | 11 | ||||||||||
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RAMPAGE Resource Report Resource Website 100+ mentions |
RAMPAGE (RRID:SCR_017590) | web service, data access protocol, analysis service resource, software resource, production service resource, service resource | 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 | 2026-02-16 09:49:16 | 124 | ||||||||||
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JWatcher Resource Report Resource Website 10+ mentions |
JWatcher (RRID:SCR_017595) | software application, data processing software, data analytics software, data analysis software, software resource, data acquisition software | 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 |
NIMH R21 MH065226; Australian Research Council ; Macquarie University |
Free, Available for download, Freely available | SCR_017595 | 2026-02-16 09:49:16 | 49 | |||||||||
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TIGS Resource Report Resource Website 1+ mentions |
TIGS (RRID:SCR_017565) | narrative resource, workflow, training material, data repository, storage service resource, service resource, data or information resource | 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 | 2026-02-16 09:49:16 | 1 | ||||||||||
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LibreOfficeCalc Resource Report Resource Website 10+ mentions |
LibreOfficeCalc (RRID:SCR_018013) | software application, data processing software, data visualization software, data analysis software, data management software, software resource | Open source software application with data analysis tools and spreadsheet templates used to manage, process and visualize data. LibreOffice Calc is spreadsheet component of LibreOffice software package developed by Document Foundation. | Data, analysis, spreadsheet, template, process, visualize | Free, Available for download, Freely available | SCR_018013 | 2026-02-16 09:49:23 | 24 | |||||||||||
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ChemRICH Resource Report Resource Website 10+ mentions |
ChemRICH (RRID:SCR_017609) | analysis service resource, web application, software resource, production service resource, service resource | 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 | 2026-02-16 09:49:16 | 17 | ||||||||
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NeuroChaT Resource Report Resource Website 1+ mentions |
NeuroChaT (RRID:SCR_018020) | software application, data processing software, software toolkit, data analysis software, software resource | Software open source python toolbox to analyse neuronal signals recorded in vivo in freely behaving animal, with particular emphasis on spatial coding. Can be used as application programming interface, or as general user interface, and is designed to help simplify adoption of standardised analyses for behavioural neurophysiology and facilitate open data sharing and collaboration between laboratories. | Neuronal signal, analysis, freely behaving animal, spatial coding, behavioural neurophysiology, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
Wellcome Trust | DOI:12688/wellcomeopenres.15533.1 | Free, Available for download, Freely available | biotools:NeuroChat | https://bio.tools/NeuroChaT | SCR_018020 | Neuron Characterisation Toolbox | 2026-02-16 09:49:23 | 2 | |||||
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PEMA Resource Report Resource Website 1+ mentions |
PEMA (RRID:SCR_017676) | software application, data processing software, software toolkit, data analysis software, software resource | Software as flexible pipeline for environmental DNA metabarcoding analysis of 16S/18S rRNA, ITS and COI marker genes. Performs reads’ pre-processing, clustering to (M)OTUs and taxonomy assignment for 16S rRNA and COI marker gene data. Allows users to explore alternative algorithms for specific steps of pipeline without need of complete re-execution. | Environmental, DNA, metabarcoding, analysis, ASVs, OTUs, 16S rRNA, COI, ITS, marker, gene, clustering, taxonomy, bio.tools |
is listed by: bio.tools is listed by: Debian |
DOI:10.1101/709113 | Free, Freely available | biotools:PEMA | https://docs.google.com/presentation/d/1lVH23DPa2NDNBhVvOTRoip8mraw8zfw8VQwbK4vkB1U/edit?fbclid=IwAR14PpWfPtxB8lLBBnoxs7UbG3IJfkArrJBS5f2kRA__kvGDUb8wiJ2Cy_s#slide=id.g57f092f54d_1_21 https://bio.tools/PEMA |
SCR_017676 | Pipeline for Environmental DNA Metabarcoding Analysis | 2026-02-16 09:49:18 | 1 | ||||||
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CNV webstore Resource Report Resource Website 1+ mentions |
CNV webstore (RRID:SCR_018007) | software application, data processing software, software toolkit, data visualization software, data analysis software, software resource, data storage software | Integrated platform to analyse, store, visualise and interpret CopyNumber Variation data. Analysis is supported for Illumina data, all CNV-reports and raw data can be imported after third-party analysis. Platform to streamline processing and downstream interpretation of microarray data in clinical context. Analysis tools include CNV analysis, parent of origin and uniparental disomy detection. Interpretation tools include data visualisation, gene prioritisation, automated PubMed searching, linking data to several genome browsers and annotation of CNVs based on several public databases. | Copy number variation, data, Illumina, CNV report, raw data, microarray data, clinical, analysis, visualization, gene prioritisation, PubMed searching, annotation, | Belgian National Fund for Scientific Research - Flanders ; Marguerite-Marie Delacroix foundation |
PMID:21208430 | http://cnv-webstore.ua.ac.be/cnv-webstore/ | SCR_018007 | CNV-webstore, CNV-WebStore | 2026-02-16 09:49:25 | 1 | ||||||||
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MicroDynamix Resource Report Resource Website 1+ mentions |
MicroDynamix (RRID:SCR_017671) | software application, data processing software, image analysis software, image reconstruction software, software resource | Software tool for dendritic spine analysis that enables to visualize and quantify spine morphology over time. After loading image data acquired at different time points from in vivo and in vitro imaging sessions, automatically aligns images in 3D, then reconstructs dendritic branches, detects dendritic spines, and identifies important metrics such as length, thickness, and overall number, for accurate quantitative comparison. | MBF Bioscience, dendritic, spine, analysis, visualize, quantify, morphology, image, data, 3D, reconstruct | Restricted | SCR_017671 | 2026-02-16 09:49:17 | 1 | |||||||||||
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EMBL-EBI COVID-19 Portal Resource Report Resource Website 10+ mentions |
EMBL-EBI COVID-19 Portal (RRID:SCR_018337) | data repository, database, storage service resource, topical portal, portal, service resource, data or information resource, disease-related portal | EMBL-EBI portal to enable researchers to upload, access and analyse COVID-19 related reference data and specialist datasets submitted to EMBL-EBI and other major centers for biomedical data. Used to facilitate data sharing and analysis to accelerate coronavirus research. The aim of the COVID-19 Data Portal is to facilitate data sharing and analysis, and to accelerate coronavirus research. EMBL-EBI and partners have set up the COVID-19 Data Portal, which will bring together relevant datasets submitted to EMBL-EBI and other major centres for biomedical data. The aim is to facilitate data sharing and analysis, and to accelerate coronavirus research. The COVID-19 Data Portal will enable researchers to upload, access and analyse COVID-19 related reference data and specialist datasets. The COVID-19 Data Portal will be the primary entry point into the functions of a wider project, the European COVID-19 Data Platform. | COVID-19, COVID-19 data, sequence, expression, protein sequence, protein structure, proteome, translatome, analysis, EMBL-EBI | is related to: EMBL-EBI Pathogens - COVID-19 | COVID-19 | Free, Freely available | SCR_018816 | https://www.covid19dataportal.org/ https://www.ebi.ac.uk/about/news/press-releases/embl-ebi-launches-covid-19-data-portal |
SCR_018337 | EMBL-EBI COVID-19 Data Portal, COVID-19 Data Portal | 2026-02-16 09:49:29 | 10 | ||||||
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Cytosplore Viewer Resource Report Resource Website 10+ mentions |
Cytosplore Viewer (RRID:SCR_018330) | web service, data access protocol, analysis service resource, software resource, production service resource, service resource | Web based interactive visual analysis system for exploration of single cell data published in Allen Cell Types Database and for number of single cell data resources of Brain Initiative Single Cell Network. Allows interactive exploration of hierarchies of cell types, visualization of transcriptome wide gene expression in combination with metadata of individual cells, performing differential analyses and statistics between manual selections of cells, or between pre-defined clusters throughout cellular hierarchy and more. | BICCN, visualization, transcriptomics, single cell data, gene expression, metadata, analysis, statistic, cellular hierarchy, Cytosplore |
uses: Allen Cell Types Database is used by: BICCN is used by: BRAIN Initiative Cell Atlas Network is related to: Allen Institute for Brain Science is related to: Leiden University; Leiden; Netherlands |
Free, Available for download, Freely available | SCR_018330 | 2026-02-16 09:49:26 | 17 | ||||||||||
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MOLEonline Resource Report Resource Website 10+ mentions |
MOLEonline (RRID:SCR_018314) | web service, data access protocol, analysis service resource, software resource, production service resource, service resource | Interactive web based tool for analyzing biomacromolecular channels, tunnels and pores. Enables two modes of calculation with one dedicated to analysis of channels and another for transmembrane pores. Can use PDB and mmCIF formats. Can analyze biomacromolecular structures stemming from NMR, X-ray and cryo-EM techniques. Interconnected with PDBe, CSA, ChannelsDB, OPM, UniProt to help setup and analysis of acquired results. Provides analytics for detection and structural characterization of channels and information about their physicochemical features. | biomacromolecular channel, analysis, biomacromolecular pore, biomacromolecular tunnel, transmembrane pore analysis, analysis, biomacromolecular sturcture, physicochemical feature |
works with: PDBe - Protein Data Bank in Europe works with: CSA - Catalytic Site Atlas works with: UniProt |
PMID:29718451 | Free, Freely available | https://mole.upol.cz/online/ | http://old.mole.upol.cz/ | SCR_018314 | MOLEonline 2.0 | 2026-02-16 09:49:26 | 30 | ||||||
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Proteomic Data Commons Resource Report Resource Website 50+ mentions |
Proteomic Data Commons (RRID:SCR_018273) | PDC | analysis service resource, data repository, database, storage service resource, production service resource, service resource, data or information resource | Portal to make cancer related proteomic datasets easily accessible to public. Facilitates multiomic integration in support of precision medicine through interoperability with other resources. Developed to advance our understanding of how proteins help to shape risk, diagnosis, development, progression, and treatment of cancer. One of several repositories within NCI Cancer Research Data Commons which enables researchers to link proteomic data with other data sets (e.g., genomic and imaging data) and to submit, collect, analyze, store, and share data throughout cancer data ecosystem. PDC provides access to highly curated and standardized biospecimen, clinical, and proteomic data, intuitive interface to filter, query, search, visualize and download data and metadata. Provides common data harmonization pipeline to uniformly analyze all PDC data and provides advanced visualization of quantitative information. Cloud based (Amazon Web Services) infrastructure facilitates interoperability with AWS based data analysis tools and platforms natively. Application programming interface (API) provides cloud-agnostic data access and allows third parties to extend functionality beyond PDC. Structured workspace that serves as private user data store and also data submission portal. Distributes controlled access data, such as patient-specific protein fasta sequence databases, with dbGaP authorization and eRA Commons authentication. | Cancer, proteomic, data, precision medicine, diagnosis, treatment, analysis, biospeciment, clinical data, metadata |
is related to: Cancer Research Data Commons has parent organization: National Cancer Institute |
cancer | Restricted | SCR_018273 | 2026-02-16 09:49:25 | 66 | ||||||||
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Interactive Repeated Experiments Dotplot Resource Report Resource Website |
Interactive Repeated Experiments Dotplot (RRID:SCR_018328) | web service, data access protocol, analysis service resource, software resource, production service resource, service resource | Web tool for creating interactive graphics. Enables authors to create interactive graphics from data obtained with repeated independent experiments. Designed for laboratory studies with repeated experiments. | Interactive graphic, repeated independent experiment, repeated experiment data, graph, analysis, dot plot | NCATS UL1 TR000135 | PMID:28974579 | Free, Freely available | SCR_018328 | 2026-02-16 09:49:28 | 0 | |||||||||
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Watchdog Resource Report Resource Website 1+ mentions |
Watchdog (RRID:SCR_018355) | software application, data processing software, data analysis software, data management software, software resource | Software workflow management system for automated and distributed analysis of large scale experimental data. Implemented in Java and is thus platform independent. | Workflow management system, automated data analysis, next generation sequencing, large scale experimental data, analysis | Free, Available for download, Freely available | https://github.com/klugem/watchdog https://anaconda.org/bioconda/watchdog-wms |
SCR_018355 | 2026-02-16 09:49:28 | 2 |
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