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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
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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/
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