R Script for the analysis of "SARS-CoV-2 Infection Induces Beta Cell Transdifferentiation "

Default Boolean Operator: Terms in a search string will be connected by the AND operator, EXAMPLE: searching genomic melanoma will produce the same results as genomic AND melanoma .
AND, OR, NOT: Combine terms in a search with the boolean operators AND (to add specificity), OR (to broaden), or NOT (to eliminate a term). Operators must be capitalized (all other search terms are not case-sensitive).
Wild Card: Add wild card symbols * (open-ended) and ? (single character) to truncate terms. EXAMPLE: searching gen* shows results for 'gene', 'genetic', 'genomic, etc. Searching gene? returns results for 'gene' or 'genes' but not for 'genome'.
Phrase Searching: Enclose search in quotation marks "keyword or search term" to search for an exact phrase. EXAMPLE: "transcription factors" returns results for records where transcription is immediately followed by the word factors .
Diacritics: Words containing diacritics translate those characters to non-diacritic form. EXAMPLE: massague returns results for Massague&#769 .
Filter by: Located on the homepage (left panel), use filters to search for records or narrow the search. From search results page, filters can be removed by clicking on the term at the top of the page.

UID: 10743

Author(s): Zhang, Tuo, Chen, Shuibing

Description: Summary from GitHub: This repository contains the R scripts necessary to perform the analysis in our paper Tang, Xuming et al. “SARS-CoV-2 Infection Induces Beta Cell Transdifferentiation.” Cell Metabolism, 19 May. 2021, doi:10.1016/j.cmet.2021.05.015, as described in the supplementary methods and main text."

Input data: "The single cell RNA-seq data were generated with the 10X Chromium and pre-processed using 10X cellranger pipeline. The raw data are available in the GEO database with accession# GSE159556."

Required R Packages: "Seurat scran scater slingshot batchelor gam future dplyr reshape2, magrittr ggplot2 pheatmap cowplot RColorBrewer"

Subject of Study

Subject(s)

Access via GitHub
R scripts
Access Restrictions: Free to All
Access Instructions: Code files are available for viewing, download, or clone through GitHub, including list of dependencies and installation instructions in the README.md
Associated Publications: Tang X, Uhl S, Zhang T, et al. SARS-CoV-2 infection induces beta cell transdifferentiation [published online ahead of print, 2021 May 19]. Cell Metab. 2021;S1550-4131(21)00232-1.
Data Type: Genomic
Equipment Used: 10X Chromium
10x Genomics' Chromium technology partitions reactions into nanoliter-scale droplets containing uniquely barcoded beads called GEMs (Gel Bead-In EMulsions). This core technology can be used to partition single cells, nuclei, or high molecular weight gDNA to prepare next generation sequencing libraries in parallel.
Dataset Format(s): R

Do you have or know of a dataset that should be added to the catalog? Let us know!