To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("Single.mTEC.Transcriptomes")

In most cases, you don't need to download the package archive at all.

Single.mTEC.Transcriptomes

 

   

Single Cell Transcriptome Data and Analysis of Mouse mTEC cells

Bioconductor version: Release (3.5)

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 at embl.de>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("Single.mTEC.Transcriptomes")

Documentation

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

browseVignettes("Single.mTEC.Transcriptomes")

 

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

Details

biocViews ExperimentData
Version 1.4.0
License LGPL
Depends
Imports
LinkingTo
Suggests DESeq2, GenomicRanges, GenomicFeatures, genefilter, statmod, gdata, RColorBrewer, ggplot2, gplots, cluster, clue, grid, gridExtra, ggbio, Gviz, geneplotter, matrixStats, pheatmap, BiocStyle, knitr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source Single.mTEC.Transcriptomes_1.4.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
Subversion source (username/password: readonly)
Package Short Url http://bioconductor.org/packages/Single.mTEC.Transcriptomes/
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