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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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The Bergen fMRI Toolbox Plugin for EEGLab Resource Report Resource Website 1+ mentions |
The Bergen fMRI Toolbox Plugin for EEGLab (RRID:SCR_016335) | data processing software, data analysis software, software toolkit, software application, software resource | Software package as a set of Matlab tools which allow the correction of fMRI-related gradient artifacts from EEG data. Designed to work within the EEGLAB environment, providing a GUI to remove fMRI gradient artifacts from the EEG. Can also be used from the Matlab command line, providing expert users with the ability to use them in custom scripts. | correct, gradient, artifact, data, electrophysiology, functional, magnetic, resonance, imaging, neuroscience |
is related to: EEGLAB is related to: MATLAB has parent organization: University of Bergen; Bergen; Norway |
Free, Available for download, Freely available | SCR_016335 | 2026-02-14 02:03:02 | 1 | ||||||||||
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Monocle2 Resource Report Resource Website 100+ mentions |
Monocle2 (RRID:SCR_016339) | data processing software, data analysis software, software toolkit, software application, software resource | Software package for analyzing single cell gene expression, classifying and counting cells, performing differential expression analysis between subpopulations of cells, and reconstructing cellular trajcectories. Works well with very large single-cell RNA-Seq experiments containing tens of thousands of cells or more. Used in computational analysis of gene expression data in single cell gene expression studies to profile transcriptional regulation in complex biological processes and highly heterogeneous cell populations. | analysis, heterogenous, population, single, cell, gene, expression, data, large, single-cell RNA-Seq, transcriptional, regulation, heterogen | NIH DP2 HD088158; Alfred P. Sloan Foundation Research Fellowship |
PMID:24658644 | Free, Available for download, Freely available | SCR_016339 | Monocle 2 | 2026-02-14 02:03:02 | 203 | ||||||||
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Electrographic Seizure Analyzer Resource Report Resource Website 1+ mentions |
Electrographic Seizure Analyzer (RRID:SCR_016344) | data analysis software, software resource, data processing software, software application | Software to automate analysis of electrographic seizures based on EEG or LFP data, featuring customizable thresholds and parameters for event detection and parameter setting. | automate, analysis, electrographic, seizure, EEG, LFP, data, event, detection, parameter, setting | is related to: MATLAB | Free, Available for download, Freely available | SCR_016344 | 2026-02-14 02:03:02 | 5 | ||||||||||
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jVenn Resource Report Resource Website 100+ mentions |
jVenn (RRID:SCR_016343) | data visualization software, data processing software, data analysis software, software application, software resource | JavaScript plug-in software application for web environments to analyze data. It is an interactive Venn diagram viewer.Used for comparing lists with Venn Diagrams. It handles up to six input lists and presents results using classical or Edwards-Venn layouts. User interactions can be controlled and customized. | analyze, data, Venn, diagram, visualisation, independent, platform | is related to: VennDiagram | Free, Available for download, Freely available | http://bioinfo.genotoul.fr/jvenn | SCR_016343 | 2026-02-14 02:03:11 | 248 | |||||||||
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Rtsne Resource Report Resource Website 100+ mentions |
Rtsne (RRID:SCR_016342) | data visualization software, data processing software, software toolkit, software application, software resource | Software as R wrapper for Van der Maaten's Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding. Used for high-dimentional data visualisation. | data, visualisation, high-dimentional, van der Maaten, Barnes-Hut, implementation, distribution, stochastic, neighbor, embedding |
is listed by: CRAN is related to: R Project for Statistical Computing is related to: University of Toronto; Ontario; Canada |
the Netherlands Organization for Scientific Research (NWO) ; European Union Seventh Framework Program |
Free, Available for download, Freely available | SCR_016900 | https://cran.r-project.org/web/packages/Rtsne/index.html | SCR_016342 | , R t-distributed stochastic neighbor embedding, R t-Distributed Stochastic Neighbor Embedding | 2026-02-14 02:03:02 | 176 | ||||||
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BioJupies Resource Report Resource Website 50+ mentions |
BioJupies (RRID:SCR_016346) | software resource, web application | Software as an open source web server that automatically generates RNA-seq data analysis of jupyter notebooks. It allows creation and containment of documents that have live code, visualizations and narrative text. | automatically, generate, RNAseq, data, analysis, notebook, create, visualize, report, custom, raw, processed, user, interface | is affiliated with: Icahn School of Medicine at Mount Sinai; New York; USA | Free, Available for download, Freely available | SCR_016346 | 2026-02-14 02:03:02 | 65 | ||||||||||
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MAST Resource Report Resource Website 50+ mentions |
MAST (RRID:SCR_016340) | MAST | data processing software, data analysis software, software toolkit, software application, software resource | Software as an open source package for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. | model, based, analysis, single, cell, transcriptomics, RNA, sequencing, data | NIH DP2 DE023321; NIBIB R01 EB008400; Bill and Melinda Gates Foundation OPP1032317 |
DOI:10.5281/zenodo.18539 | Free, Available for download, Freely available | https://github.com/RGLab/MAST/ | SCR_016340 | Model based Analysis of Single Cell Transcriptomics | 2026-02-14 02:03:14 | 86 | ||||||
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Interactive Line Graph Resource Report Resource Website |
Interactive Line Graph (RRID:SCR_018334) | web service, data analysis service, analysis service resource, production service resource, service resource, data access protocol, software resource | Interactive web based tool for creating line graphs for scientific publications. Users can view different summary statistics, examine lines for any individual in data, focus on time points or groups of interest, and view changes between any two time points and conditions. | Line graph, scientific publication, summary statistics, examine lines, time point, changes between time points, data, statistic, plot | NCI P50 AG44170; Office of Research on Women Health |
PMID:27332507 | Free, Freely available | SCR_018334 | 2026-02-14 02:03:36 | 0 | |||||||||
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PlotsOfData Resource Report Resource Website 10+ mentions |
PlotsOfData (RRID:SCR_018333) | web service, data analysis service, analysis service resource, production service resource, service resource, data access protocol, software resource | Web app for visualizing data together with their summaries. Visualizes data and statistics to enable comparison of experimental conditions. Written in R and uses packages including shiny, ggplot2, dplyr, tidyr, readr, magrittr, ggbeeswarm, readxl, DT. Github page of PlotsOfData can be used to trace changes between different versions. | Data visualization, data statistics, comparison between samples, plot, graph, data |
uses: Shiny uses: R Project for Statistical Computing uses: RStudio uses: ggplot2 uses: dplyr uses: tidyr is related to: BoxPlotR |
PMID:30917112 | Free, Freely available | https://github.com/JoachimGoedhart/PlotsOfData | SCR_018333 | 2026-02-14 02:03:31 | 34 | ||||||||
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CoronaVIR Resource Report Resource Website 1+ mentions |
CoronaVIR (RRID:SCR_018338) | disease-related portal, data or information resource, portal, topical portal | Web based platform on COVID-19 to maintain predicted diagnostic, drug and vaccine candidates and computational resources on novel coronavirus SARS-CoV-2 and its resulting disease COVID-19. Provides collected and organized information from literature and other resources from internet, links to appropriate literature . Integrated multi-omics repository dedicated to current genomic, proteomic, diagnostic and therapeutic knowledge about coronaviruses. | COVID-19, SARS-CoV-2, diagnostic, drug, candidate, computational resource. coronavirus, disease, literature, genomic, proteomic, data | COVID-19 | DOI:10.31219/osf.io/xegzu | Free, Freely available | SCR_018351 | SCR_018338 | 2026-02-14 02:03:31 | 4 | ||||||||
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American Diabetes Association COVID-19 Resources and Webinar Series Resource Report Resource Website |
American Diabetes Association COVID-19 Resources and Webinar Series (RRID:SCR_018346) | disease-related portal, data or information resource, portal, topical portal | Web page created by American Diabetes Association. Contains resources and information about COVID-19 for diabetes professionals and patients. ADA also provides online forum, webinar series and podcast. Online forum to exchange questions, answers, and best practices with leading clinicians from diabetes community. All ADA members can contribute, and any interested health professional can read forum and responses. | COVID-19, American Diabetes Association, diabetes, diabetes professional, diabetes patient, forum, webinar, podcast, data | COVID-19, Diabetes | Restricted | SCR_018346 | COVID-19 and Diabetes | 2026-02-14 02:03:19 | 0 | |||||||||
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EMBL-EBI Pathogens - COVID-19 Resource Report Resource Website |
EMBL-EBI Pathogens - COVID-19 (RRID:SCR_018343) | disease-related portal, data or information resource, portal, topical portal | Data collection related to COVID-19 held at EMBL-EBI , including sequences of outbreak isolates and records related to coronavirus biology, protein expression, protein sequence, protein structure, proteome and translatome data and literature. | COVID-19, COVID-19 data, EMBL-EBI, sequences of outbreak isolates, coronavirus, protein expression, protein sequence, protein structure, proteome, translatome, data, COVID-19 literature | is related to: EMBL-EBI COVID-19 Portal | COVID-19 | Free, Freely available | SCR_018343 | 2026-02-14 02:03:31 | 0 | |||||||||
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2019 Novel Coronavirus Resource (2019nCoVR) by China National Center for Bioinformation Resource Report Resource Website 1+ mentions |
2019 Novel Coronavirus Resource (2019nCoVR) by China National Center for Bioinformation (RRID:SCR_018342) | 2019nCoVR | disease-related portal, data or information resource, portal, topical portal | Bioinformation related to COVID-19. Site developed and maintained by China National Center for Bioinformation. Collection of sequences, genome variations, publication, clinical resource data. | COVID-19, sequence, genome sequence, genome variation, data, China National Center for Bioinformation | COVID-19 | Free, Freely available | SCR_018342 | 2019 Novel Coronavirus Resource, 2019 Novel Coronavirus Resource (2019nCoVR), CNCB 2019nCoVR, CNCB 2019 Novel Coronavirus Resource | 2026-02-14 02:03:34 | 4 | ||||||||
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Proteomic Data Commons Resource Report Resource Website 50+ mentions |
Proteomic Data Commons (RRID:SCR_018273) | PDC | data repository, storage service resource, analysis service resource, data or information resource, production service resource, service resource, database | 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 | 2026-02-14 02:03:18 | 66 | ||||||||
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SARS-CoV-2-Sequences Resource Report Resource Website 10+ mentions |
SARS-CoV-2-Sequences (RRID:SCR_018319) | data repository, storage service resource, data set, data or information resource, service resource | Collection of SARS-CoV-2 sequences currently available in GenBank genetic sequence database and Sequence Read Archive. Updated as additional sequences are released. | SARS-CoV-2, SARS coronavirus, SARS-CoV infection, Coronavirus, data, SARS-CoV-2 sequence collection, nucleotide, genome, Betacoronavirus, protein |
works with: GenBank works with: NCBI Sequence Read Archive (SRA) |
COVID-19 | The Federal Government | Free, Available for download, Freely available | SCR_018319 | Severe Acute Respiratory Syndrome CoronaVirus 2 Sequences | 2026-02-14 02:03:36 | 28 | |||||||
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Global Initiative on Sharing All Influenza Data Resource Report Resource Website 1000+ mentions |
Global Initiative on Sharing All Influenza Data (RRID:SCR_018251) | GISAID | portal, data or information resource, disease-related portal, topical portal, database | Portal to share hCoV-19 genome sequences. Collection of genome sequences and related clinical and epidemiological data associated with coronavirus hCoV-19. Global repository of SARS-CoV-2 genomes. Initiative involves public-private-partnerships between Freunde of GISAID and governments of Federal Republic of Germany, Singapore and United States of America, with support from private and corporate philanthropy.International database of hCoV-19 genome sequences and related clinical and epidemiological data. Resource for influenza and hCoV-19 data. | hCoV19, hCoV-19 genome sequence, data, coronavirus, SARS coronavirus, Coronavirus, genome, genome database, influenza, SARS-CoV infection, SARS-CoV-2, COVID-19 |
lists: Health Data Research UK COVID-19 Initiative is listed by: Data and Computational Resources to Address COVID-19 is related to: SARS-CoV-2 mutation effects and 3D structure prediction from sequence covariation works with: Nextstrain |
CoV19, COVID19, COVID-19 | PMID:28382917 | Restricted | SCR_018279, r3d100010126, SCR_018318 | https://doi.org/10.17616/R3Q59F | SCR_018251 | 2026-02-14 02:03:29 | 1964 | |||||
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COVID-19 Crowd Generated Gene and Drug Set Library Resource Report Resource Website 1+ mentions |
COVID-19 Crowd Generated Gene and Drug Set Library (RRID:SCR_018252) | data repository, storage service resource, web service, data or information resource, service resource, data access protocol, software resource, database | Software tool as interface to submit, serve, and analyze COVID19 related gene and drug sets. Collection of gene and drug sets related to COVID-19 research contributed by community. | COVID-19 data collection, gene collection, drug set collection, data, COVID-19 | has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA | COVID-19, COVID19 | Free, Freely available | https://github.com/MaayanLab/covid19_crowd_library | SCR_018252 | 2026-02-14 02:03:35 | 3 | ||||||||
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TDimpute Resource Report Resource Website 1+ mentions |
TDimpute (RRID:SCR_018306) | data analysis software, software resource, data processing software, software application | Software tool to transfer learning based deep neural network to impute missing gene expression data from DNA methylation data. | Transfer learning; gene expression prediction; DNA methylation; TCGA, neural network, missing gene expression, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/803692 | Free, Available for download, Freely available | biotools:tDimpute, BioTools:TDimpute | https://bio.tools/TDimpute https://bio.tools/TDimpute https://bio.tools/TDimpute |
SCR_018306 | 2026-02-14 02:03:19 | 1 | |||||||
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GLYCAM-Web Resource Report Resource Website 50+ mentions |
GLYCAM-Web (RRID:SCR_018260) | web service, portal, data or information resource, data access protocol, software resource, topical portal | Web provides tools for modeling 3D structures of molecules and complexes containing carbohydrates including oligosaccharide conformation modeling and glycoprotein 3D structure modeling. Used to simplify prediction of three dimensional structures of carbohydrates and macromolecular structures involving carbohydrates. | Glycosylated SARS-Cov-2 Spike protein, SARS-Cov-2, SARS-Cov-2 Spike protein, spike protein, 3D structure, carbohydrate, oligosaccharide conformation, modeling, structure modeling, data | has parent organization: University of Georgia; Georgia; USA | COVID-19, COVID19 | NIH | Free, Freely available | SCR_018260 | GLYCAM | 2026-02-14 02:03:18 | 96 | |||||||
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biomod2 Resource Report Resource Website 50+ mentions |
biomod2 (RRID:SCR_018246) | data analysis software, software resource, data processing software, software application | Software R package for species distribution modeling, calibration and evaluation, ensemble of models, ensemble forecasting and visualization. | species distribution modeling, ensemble of models, ensemble forecasting, visualization, data | is listed by: CRAN | Free, Available for download, Freely available | SCR_018246 | 2026-02-14 02:03:35 | 55 |
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