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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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COVID-19 and Coronavirus plasmids and resources Resource Report Resource Website 1+ mentions |
COVID-19 and Coronavirus plasmids and resources (RRID:SCR_018347) | catalog, data or information resource, database | Collections of Addgene plasmids, open access articles, protocols, and other resource collections related to COVID-19 that may be of use to scientists. Ordering or depositing plasmids related to COVID-19 research. | Plasmid, COVID-19, SARS-CoV-2 plasmid, plasmid order, Adddgene, COVID-19 plasmid repository, COVID-19 related article, COVID-19 related protocol, COVID-19 resource collection, data | COVID-19 | Free, Freely available | SCR_018347 | 2026-09-05 06:30:09 | 1 | ||||||||||
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Fitness Browser Resource Report Resource Website 1+ mentions |
Fitness Browser (RRID:SCR_018981) | data access protocol, data or information resource, software resource, web service | Web tool for browsing genome wide fitness experiments for diverse bacteria from Deutschbauer lab, the Arkin lab, and collaborators. Collection of mutant phenotypes for bacterial genes of unknown function. | Genome browser, bacteria, mutant phenotype, bacterial genes, unknown function, data | has parent organization: University of California at Berkeley; Berkeley; USA | NCRR S10 RR027303; NCRR S10 RR029668; NIH Office of the Director OD018174; Office of Science of the US Department of Energy |
PMID:29769716 | Free, Freely available | SCR_018981 | 2026-09-05 06:30:10 | 9 | ||||||||
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cRAP protein sequences Resource Report Resource Website 100+ mentions |
cRAP protein sequences (RRID:SCR_018187) | cRAP | data or information resource, data repository, database, service resource, storage service resource | List of proteins commonly found in proteomics experiments that are present either by accident or through unavoidable contamination of protein samples. List is based on analysis of current version of GPMDB, as well as suggestions by users. Current version of cRAP in FASTA format can be obtained from the GPM FTP site. | Protein, collection, proteomic experiment, protein sample, contamination, Global Proteome Machine Data Base, data repository, data, FASEB list | THIS RESOURCE IS NO LONGER IN SERVICE | ftp://ftp.thegpm.org/fasta/cRAP | SCR_018187 | common Repository of Adventitious Proteins | 2026-09-05 06:30:09 | 198 | ||||||||
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Loupe Browser Resource Report Resource Website 100+ mentions |
Loupe Browser (RRID:SCR_018555) | data analysis software, data processing software, software application, software resource | Desktop application that provides interactive visualization functionality to analyze data from different 10x Genomics solutions. Used to interrogate different views of 10x data to gain insights into underlying biology. | Interactive visualization, data analysis, 10x Genomics solutions, data | works with: Cell Ranger | Restricted | SCR_018555 | Loupe Cell Browser 4.0 | 2026-09-05 06:30:10 | 187 | |||||||||
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Coronavirus Immunotherapy Consortium Resource Report Resource Website 10+ mentions |
Coronavirus Immunotherapy Consortium (RRID:SCR_018258) | CoVIC | consortium, data or information resource, organization portal, portal, topical portal | Consortium to unite efforts and resources from experts across globe to advance effective, antibody based therapies against novel coronavirus, SARS-CoV-2. Represents multidisciplinary convergence of structural biology, virologists, immunologists, clinicians and bioinformaticians from academic and industry settings. Collects antibodies for testing as part of CoVICS. Contributed antibodies are blinded and will only be known as code name. Antibody contributors will be able to see performance of their own molecules and take part in analysis. Contributors retain ownership of their antibodies and may continue to publish on them using original antibody names. Goal is to determine relative in vitro potency and in vivo efficacy using centralized standardized assays to identify best individual mAbs and rational combinations of mAbs. Consortium will recommend ideal therapeutic molecules for human use to protect vulnerable populations from COVID-19 disease. CoVIC database (CoVIC-DB) will serve as clearinghouse for monoclonal antibodies against SARS-CoV-2. Database will catalog contributed antibodies in searchable resource and provide interactive analysis tools for comparisons among them. | COVID-19, antibody, antibody based therapy, coronavirus, SARS-CoV-2, antibody collection, analysis, potency in vitro, efficacy in vivo, standardized assay, identify mAb, therapeutic molecule, vulnerable population protect, database, data |
is related to: La Jolla Institute for Immunology is related to: Duke University; North Carolina; USA is related to: CoVIC-DB Database |
COVID-19 | Free, Freely available | SCR_018258 | 2026-09-05 06:30:09 | 14 | ||||||||
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METAGENOTE Resource Report Resource Website 1+ mentions |
METAGENOTE (RRID:SCR_018494) | data access protocol, software resource, web service | Quick and intuitive way to annotate data from genomics studies including microbiome. Project to aid researchers in applying standardized metadata describing what, where, how, and when of samples collected in genomics study. Collection of METAdata of GEnomics studies on web based NOTEbook. Metadata are stored in centralized repository and validated according to guidelines from Genomics Standard Consortium, which are also supported by repositories and large microbiome initiatives such as NCBI, European Bioinformatics Institute (EBI), and Earth Microbiome Project. Upon request from researchers, data will also be submitted for publication via NCBI Sequence Read Archive (SRA) repository. | Annotate data, genomics study, microbiome, metadata, genomics, data |
is related to: NCBI Sequence Read Archive (SRA) is related to: NCBI |
NIH | Free, Freely available | SCR_018494 | METAdata of GEnomics studies on a web based NOTEbook | 2026-09-05 06:30:10 | 1 | ||||||||
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Stanford University Human Immune Monitoring Center Core Facility Resource Report Resource Website 1+ mentions |
Stanford University Human Immune Monitoring Center Core Facility (RRID:SCR_018266) | HIMC | access service resource, core facility, data or information resource, service resource | Core designed for immune monitoring services for clinical and translational studies. Goals include providing standardized, state-of-the art immune monitoring assays at RNA, protein, and cellular level, testing and developing new technologies for immune monitoring, archive, report, and mine data from immune monitoring studies. HIMC uses online database for integration of data from standard HIMC assays, along with de-identified clinical and demographic data. | Immune monitoring serivce, clinical study, translational study, RNA, protein, data, core facility, USEDit, ABRF |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: Stanford University; Stanford; California |
Open | ABRF_399 | https://coremarketplace.org/?FacilityID=399 | SCR_018266 | Stanford University - Human Immune Monitoring Center, Human Immune Monitoring Center (HIMC) | 2026-09-05 06:30:09 | 1 | ||||||
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Optimus Pipeline Resource Report Resource Website 1+ mentions |
Optimus Pipeline (RRID:SCR_018908) | data analysis software, data processing software, software application, software resource | Optimus is a pipeline developed by the Data Coordination Platform (DCP) of the Human Cell Atlas (HCA) Project that supports processing of any 3' single-cell and single-nuclei expression data generated with the 10x Genomic v2 or v3 assay. It is an alignment and transcriptome quantification pipeline that corrects cell barcodes, aligns reads to the genome, corrects Unique Molecular Identifiers (UMIs), generates an expression matrix in a UMI-aware manner, calculates summary metrics for genes and cells, detects empty droplets, returns read outputs in BAM format, and returns gene counts in NumPy matrix and Loom matrix formats. | Data, single cell data, 10x technology data, cell bar code correction pipeline, reads alignment, genome, unique molecular identifier correction, mouse data sets analysis, human data sets analysis, |
is used by: BICCN is related to: Human Cell Atlas |
Free, Available for download, Freely available | https://github.com/broadinstitute/warp/tree/master/pipelines/skylab/optimus | SCR_018908 | Optimus | 2026-09-05 06:30:10 | 2 | ||||||||
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ClusPro Resource Report Resource Website 500+ mentions |
ClusPro (RRID:SCR_018248) | data access protocol, service resource, software resource, web service | Web tool for protein-protein docking. Server provides removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering data, and location of heparin-binding sites. Six different energy functions can be used, depending on protein type.This protocol describes use of various options, construction of auxiliary restraints files, selection of energy parameters, and analysis of results. | Protein-protein docking, protein structure, energy function, energy parameter selection, analysis, data |
has parent organization: Boston University; Massachusetts; USA has parent organization: Stony Brook University; New York; USA |
NIGMS R01 GM061867; NIGMS R35 GM118078 |
PMID:28079879 | Free, Freely available | SCR_018248 | ClusPro 2.0 | 2026-09-05 06:30:09 | 979 | |||||||
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Fractalis Resource Report Resource Website 1+ mentions |
Fractalis (RRID:SCR_016362) | analysis service resource, data access protocol, data analysis service, data processing software, data visualization software, production service resource, service resource, software application, software library, software resource, software toolkit, web service | Software as a scalable open-source service for platform-independent interactive visual analysis of biomedical data. It is a service and a library that work in tandem to equip existing platforms with visual analytical capabilities for explorative data analysis. | platform, independent, interactive, visual, analysis, biomedical, data, library | Luxembourg Ministry of Higher Education and Research ; National Centre of Excellence in Research on Parkinson’s disease NCER13/BM/11264123 |
Free, Available for download, Freely available | https://git-r3lab.uni.lu/Fractalis/fractalis/blob/master/README.md | SCR_016362 | 2026-09-05 06:28:07 | 1 | |||||||||
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lilikoi Resource Report Resource Website 1+ mentions |
lilikoi (RRID:SCR_016361) | data analysis software, data processing software, software application, software resource, software toolkit | Software tool as an R package for personalized pathway-based classification modeling using metabolomics data. Provides personalized pathway deregulation measurements (PDS scores) and offers a standardized classification model for biomarker prediction. | personalized, medicine, metabolomics, data, classification, clustering, biomarker, prediction, algorithm, calculating, microarray, enrichment |
is listed by: OMICtools is related to: University of Hawaii; Hawaii; USA |
NICHD R01 HD084633; NIEHS K01 ES025434; NIGMS GM103457; NLM R01 LM012373 |
DOI:https://doi.org/10.1101/283408 | Free, Available for download, Freely available | https://omictools.com/lilikoi-tool | SCR_016361 | 2026-09-05 06:28:07 | 3 | |||||||
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The Pancreatic Beta-Cell Consortium Resource Report Resource Website 1+ mentions |
The Pancreatic Beta-Cell Consortium (RRID:SCR_016328) | PBC Consortium | data or information resource, data repository, disease-related portal, portal, service resource, storage service resource, topical portal | Portal to provide a repository for beta-cell data, to connect researchers from different backgrounds interested in contributing data, models and/or ideas for new insights into beta-cell biology. Used to understand beta-cell biology and diabetes through a cross-disciplinary approach for the assembly of spatiotemporal multi-scale whole cell models of human pancreatic beta-cells. | repository, pancreatic, Bcell, data, whole, cell, model, human, connect, contribute, model, idea, diabetes, integrate, approach, computation, design, effective, treatment, experiment, biology |
is related to: University of Southern California; Los Angeles; USA is related to: California Institute of Technology; Division of Biology is related to: University of California at Berkeley; Berkeley; USA is related to: Scripps Research Institute |
Diabetes | SCR_016328 | Pancreatic B Cell Consortium | 2026-09-05 06:28:07 | 5 | ||||||||
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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 analysis software, data processing software, software application, software resource, software toolkit | 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 | 2026-09-05 06:28:07 | 1 | ||||||||||
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Monocle2 Resource Report Resource Website 100+ mentions |
Monocle2 (RRID:SCR_016339) | data analysis software, data processing software, software application, software resource, software toolkit | 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 | Alfred P. Sloan Foundation Research Fellowship ; NIH DP2 HD088158 |
PMID:24658644 | Free, Available for download, Freely available | SCR_016339 | Monocle 2 | 2026-09-05 06:28:07 | 227 | ||||||||
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Electrographic Seizure Analyzer Resource Report Resource Website 1+ mentions |
Electrographic Seizure Analyzer (RRID:SCR_016344) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-05 06:28:07 | 5 | ||||||||||
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jVenn Resource Report Resource Website 100+ mentions |
jVenn (RRID:SCR_016343) | data analysis software, data processing software, data visualization 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 | 2026-09-05 06:28:07 | 348 | |||||||||
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Rtsne Resource Report Resource Website 100+ mentions |
Rtsne (RRID:SCR_016342) | data processing software, data visualization software, software application, software resource, software toolkit | 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 |
European Union Seventh Framework Program ; the Netherlands Organization for Scientific Research (NWO) |
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 | 2026-09-05 06:28:07 | 190 | ||||||
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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 | 2026-09-05 06:28:07 | 72 | ||||||||||
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MAST Resource Report Resource Website 100+ mentions |
MAST (RRID:SCR_016340) | MAST | data analysis software, data processing software, software application, software resource, software toolkit | 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 | Bill and Melinda Gates Foundation OPP1032317; NIBIB R01 EB008400; NIH DP2 DE023321 |
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 | 2026-09-05 06:28:07 | 106 | ||||||
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MGnify Resource Report Resource Website 50+ mentions |
MGnify (RRID:SCR_016429) | data or information resource, data repository, portal, service resource, storage service resource | Portal for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. Provides functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets held within the European Nucleotide Archive (ENA).Microbiome analysis resource in 2020. | analysis, exploration, metagenomic, metatranscriptomic, amplicon, assembly, data, sequence, ENA, microbial, population, environment, bio.tools |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: Debian is listed by: bio.tools is related to: NIDDK Information Network (dkNET) |
EMBL ; EU Seventh Framework Programme for Research MICROB3; InnovateUK 102513; Research Councils UK (RCUK) ; the Biotechnology and Biological Sciences Research Council (BBSRC) BBM0117551; the Biotechnology and Biological Sciences Research Council (BBSRC) BBN0183541; the Biotechnology and Biological Sciences Research Council BBI02612X1; the Biotechnology and Biological Sciences Research Council BBM0117551; the European Commission within the Research Infrastructures programme of Horizon 2020 676559 |
PMID:31696235 | Free, Freely available, Training online available | r3d100011192, biotools:MGnify | https://bio.tools/MGnify, https://doi.org/10.17616/R34W68 | SCR_016429 | , MGnify, EBI Metagenomics | 2026-09-05 06:28:08 | 74 |
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