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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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, catalog, portal, data or information resource, database | 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 | 2026-07-30 09:30:12 | 1000 | ||||||||
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iBright Analysis Software Resource Report Resource Website 10+ mentions |
iBright Analysis Software (RRID:SCR_017632) | data processing software, data analysis software, software resource, image analysis software, software application | 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 | 2026-07-30 09:30:22 | 17 | |||||||||||
|
Mesquite Resource Report Resource Website 100+ mentions |
Mesquite (RRID:SCR_017994) | data processing software, software application, data analysis software, software resource | Software tool as modular system for evolutionary analysis. Software for evolutionary biology, designed to organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Analyses available depend on modules installed. Comes with many packages already installed. | Modular, evolutionary, analysis, organize, comparative data, organism, phylogenetic, population genetic, non-pylogenetic | is listed by: Debian | NSF DEB 1258220; David and Lucile Packard Foundation ; NSERC Discovery grant ; NSF |
Free, Available for download, Freely available | https://sources.debian.org/src/mesquite/ | SCR_017994 | Mesquite 3.04, Mesquite 3.61 | 2026-07-30 09:30:17 | 151 | |||||||
|
VG Studio MAX Resource Report Resource Website 10+ mentions |
VG Studio MAX (RRID:SCR_017997) | data processing software, data analysis software, data visualization software, software resource, software application | 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 | 2026-07-30 09:30:24 | 11 | ||||||||||
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LibreOfficeCalc Resource Report Resource Website 10+ mentions |
LibreOfficeCalc (RRID:SCR_018013) | data processing software, data management software, data analysis software, data visualization software, software resource, software application | 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 | 2026-07-30 09:30:29 | 24 | |||||||||||
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NeuroChaT Resource Report Resource Website 1+ mentions |
NeuroChaT (RRID:SCR_018020) | data processing software, software toolkit, data analysis software, software resource, software application | 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 | 2026-07-30 09:30:24 | 2 | |||||
|
PEMA Resource Report Resource Website 1+ mentions |
PEMA (RRID:SCR_017676) | data processing software, software toolkit, data analysis software, software resource, software application | 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 | 2026-07-30 09:30:13 | 1 | ||||||
|
DichroWeb Resource Report Resource Website 50+ mentions |
DichroWeb (RRID:SCR_018125) | service resource, data access protocol, data analysis service, software resource, web service, production service resource, analysis service resource | Web server for analysis of protein circular dichroism spectra. Provides access to circular dichroism secondary structure calculation algorithms and reference databases. Used in analysis of protein secondary structures. | Analysis, protein, circular dichroism spectra, secondary structure, reference database, algorithm, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of London; London; United Kingdom |
BBSRC | PMID:17896349 PMID:15215473 |
Restricted | biotools:dichroweb | https://bio.tools/dichroweb | SCR_018125 | 2026-07-30 09:30:25 | 62 | ||||||
|
CNV webstore Resource Report Resource Website 1+ mentions |
CNV webstore (RRID:SCR_018007) | data processing software, software toolkit, data analysis software, data visualization software, software resource, data storage software, software application | 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 | 2026-07-30 09:30:29 | 1 | ||||||||
|
MicroDynamix Resource Report Resource Website 1+ mentions |
MicroDynamix (RRID:SCR_017671) | data processing software, software resource, image reconstruction software, image analysis software, software application | 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 | 2026-07-30 09:30:17 | 1 | |||||||||||
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EMBL-EBI COVID-19 Portal Resource Report Resource Website 10+ mentions |
EMBL-EBI COVID-19 Portal (RRID:SCR_018337) | service resource, data repository, disease-related portal, portal, topical portal, data or information resource, database, storage service resource | 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 | 2026-07-30 09:30:22 | 10 | ||||||
|
Cytosplore Viewer Resource Report Resource Website 10+ mentions |
Cytosplore Viewer (RRID:SCR_018330) | service resource, data access protocol, software resource, web service, production service resource, analysis 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 | 2026-07-30 09:30:21 | 17 | ||||||||||
|
MOLEonline Resource Report Resource Website 10+ mentions |
MOLEonline (RRID:SCR_018314) | service resource, data access protocol, software resource, web service, production service resource, analysis 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 | 2026-07-30 09:30:33 | 30 | ||||||
|
Proteomic Data Commons Resource Report Resource Website 50+ mentions |
Proteomic Data Commons (RRID:SCR_018273) | PDC | service resource, data repository, data or information resource, database, storage service resource, analysis service resource, production service 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 | 2026-07-30 09:30:21 | 66 | ||||||||
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Interactive Repeated Experiments Dotplot Resource Report Resource Website |
Interactive Repeated Experiments Dotplot (RRID:SCR_018328) | service resource, data access protocol, software resource, web service, production service resource, analysis 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 | 2026-07-30 09:30:33 | 0 | |||||||||
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Watchdog Resource Report Resource Website 1+ mentions |
Watchdog (RRID:SCR_018355) | data processing software, data management software, data analysis software, software resource, software application | 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 | 2026-07-30 09:30:34 | 2 | ||||||||||
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SoftBerry Resource Report Resource Website 100+ mentions |
SoftBerry (RRID:SCR_000902) | data or information resource, software resource, portal | Developer of software tools for genomic research focused on computational methods of high throughput biomedical data analysis, including software to support next generation sequencing technologies, transcriptome analysis with RNASeq data, SNP detection and selection of disease specific SNP subsets. Provides custom genome annotation services. | genomic, analysis, computation, biomedical, data analysis, rnaseq, sna, snp, transcriptome | Restricted | nlx_156881 | http://linux1.softberry.com/ | SCR_000902 | Linux SoftBerry, Soft berry | 2026-07-30 09:26:05 | 356 | ||||||||
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Net Station API Resource Report Resource Website |
Net Station API (RRID:SCR_000867) | Net Station API | application programming interface, data access protocol, software resource, commercial organization | APIs for Net Station data files. APIs are available for C++, C#, and Java. | eeg, meg, electrocorticography, c++, java, visualization, analysis, presentation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Net Station EEG Software |
Free, Available for download, Freely available | nlx_155824 | http://www.nitrc.org/projects/netstation_api | SCR_000867 | Net Station Software for EEG Acquisition and Physician and Review | 2026-07-30 09:26:03 | 0 | ||||||
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RDPipeline Resource Report Resource Website 10+ mentions |
RDPipeline (RRID:SCR_001192) | RDPipeline | software resource, software application, data processing software | Software to simplify the processing of large rRNA sequence libraries (including single-strand and paired-end reads) obtained through high-throughput sequencing technology. Tools for assembly, quality filtering, taxonomy based analysis and taxonomy independent analysis tools, and tools to convert the data to formats suitable for common ecological and statistical packages are available. For extremely large datasets, command line tools are available. | amplicon sequencing, high-throughput sequencing, rrna, assembly, quality filtering, taxonomy, analysis, FASEB list |
is listed by: OMICtools has parent organization: Ribosomal Database Project |
PMID:24288368 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02158 | SCR_001192 | RDP Pipeline, RDP Amplicon Sequence Pipeline | 2026-07-30 09:26:11 | 39 | ||||||
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STRAP Resource Report Resource Website 100+ mentions |
STRAP (RRID:SCR_005675) | STRAP | software resource, software application, data processing software | Software program that automatically annotates a protein list with information that helps in the meaningful interpretation of data from mass spectrometry and other techniques. It takes protein lists as input, in the form of plain text files, protXML files (usually from the TPP), or Dat files from MASCOT search results. From this, it generates protein annotation tables, and a variety of GO charts to aid individual and differential analysis of proteomics data. It downloads information from mainly the Uniprot and EBI QuickGO databases. STRAP requires Windows XP or higher with at least version 3.5 of the Microsoft .NET Framework installed. Platform: Windows compatible | protein, gene, annotation, mass spectrometry, proteomics, visualization, browser, differential analysis, analysis, ontology or annotation browser, ontology or annotation visualization, differential analysis of proteomics data sets, windows, protein annotation, data visualization, c#, pathway, FASEB list |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: UniProt is related to: QuickGO has parent organization: Boston University School of Medicine; Massachusetts; USA |
NHLBI contract N01 HV28178; NCRR P41 RR10888 |
PMID:19839595 | Open unspecified license, Acknowledgement requested | OMICS_02277, nlx_149115 | SCR_005675 | Software Tool for Rapid Annotation of Proteins, STRAP for GO Annotation, STRAP - Software Tool for Rapid Annotation of Proteins | 2026-07-30 09:27:14 | 120 |
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