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https://www.addgene.org/collections/covid-19-resources/
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.
Proper citation: COVID-19 and Coronavirus plasmids and resources (RRID:SCR_018347) Copy
http://fit.genomics.lbl.gov/cgi-bin/myFrontPage.cgi
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.
Proper citation: Fitness Browser (RRID:SCR_018981) Copy
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.
Proper citation: cRAP protein sequences (RRID:SCR_018187) Copy
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.
Proper citation: Loupe Browser (RRID:SCR_018555) Copy
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.
Proper citation: Coronavirus Immunotherapy Consortium (RRID:SCR_018258) Copy
https://metagenote.niaid.nih.gov/
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.
Proper citation: METAGENOTE (RRID:SCR_018494) Copy
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.
Proper citation: Stanford University Human Immune Monitoring Center Core Facility (RRID:SCR_018266) Copy
https://broadinstitute.github.io/warp/docs/Pipelines/Optimus_Pipeline/README
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.
Proper citation: Optimus Pipeline (RRID:SCR_018908) Copy
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.
Proper citation: ClusPro (RRID:SCR_018248) Copy
https://fractalis.lcsb.uni.lu/
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.
Proper citation: Fractalis (RRID:SCR_016362) Copy
https://github.com/lanagarmire/lilikoi
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.
Proper citation: lilikoi (RRID:SCR_016361) Copy
https://www.pbcconsortium.org/
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.
Proper citation: The Pancreatic Beta-Cell Consortium (RRID:SCR_016328) Copy
http://fmri.uib.no/index.php?option=com_content&view=article&id=53&Itemid=78
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.
Proper citation: The Bergen fMRI Toolbox Plugin for EEGLab (RRID:SCR_016335) Copy
http://cole-trapnell-lab.github.io/monocle-release/docs/
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.
Proper citation: Monocle2 (RRID:SCR_016339) Copy
https://github.com/KM-Lab/Electrographic-Seizure-Analyzer
Software to automate analysis of electrographic seizures based on EEG or LFP data, featuring customizable thresholds and parameters for event detection and parameter setting.
Proper citation: Electrographic Seizure Analyzer (RRID:SCR_016344) Copy
http://jvenn.toulouse.inra.fr/app/example.html
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.
Proper citation: jVenn (RRID:SCR_016343) Copy
https://github.com/jkrijthe/Rtsne
Software as R wrapper for Van der Maaten's Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding. Used for high-dimentional data visualisation.
Proper citation: Rtsne (RRID:SCR_016342) Copy
https://amp.pharm.mssm.edu/biojupies/
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.
Proper citation: BioJupies (RRID:SCR_016346) Copy
https://bioconductor.org/packages/release/bioc/html/MAST.html
Software as an open source package for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.
Proper citation: MAST (RRID:SCR_016340) Copy
https://www.ebi.ac.uk/metagenomics/
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.
Proper citation: MGnify (RRID:SCR_016429) Copy
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