Single.mTEC.Transcriptomes

Single Cell Transcriptome Data and Analysis of Mouse mTEC cells

Bioconductor version: Release (3.17)

This data package contains the code used to analyse the single-cell RNA-seq and the bulk ATAC-seq data from the manuscript titled: Single-cell transcriptome analysis reveals coordinated ectopic-gene expression patterns in medullary thymic epithelial cells. This paper was published in Nature Immunology 16,933-941(2015). The data objects provided in this package has been pre-processed: the raw data files can be downloaded from ArrayExpress under the accession identifiers E-MTAB-3346 and E-MTAB-3624. The vignette of this data package provides a documented and reproducible workflow that includes the code that was used to generate each statistic and figure from the manuscript.

Author: Alejandro Reyes

Maintainer: Alejandro Reyes <alejandro.reyes.ds at gmail.com>

Citation (from within R, enter citation("Single.mTEC.Transcriptomes")):

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Single.mTEC.Transcriptomes")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("Single.mTEC.Transcriptomes")

Analysis of single cell mTEC data.	PDF	R Script
Reference Manual	PDF

Details

biocViews	ExperimentData
Version	1.28.0
License	LGPL
Depends	R (>= 3.5.0)
Imports
Linking To
Suggests	DESeq2, GenomicRanges, GenomicFeatures, genefilter, statmod, gdata, RColorBrewer, ggplot2, gplots, cluster, clue, grid, gridExtra, ggbio, Gviz, geneplotter, matrixStats, pheatmap, BiocStyle, knitr, BiocParallel
System Requirements
Enhances
URL

Depends On Me
Imports Me
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	Single.mTEC.Transcriptomes_1.28.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/Single.mTEC.Transcriptomes
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Single.mTEC.Transcriptomes
Package Short Url	https://bioconductor.org/packages/Single.mTEC.Transcriptomes/
Package Downloads Report	Download Stats