Single.mTEC.Transcriptomes
This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see Single.mTEC.Transcriptomes.
Single Cell Transcriptome Data and Analysis of Mouse mTEC cells
Bioconductor version: 3.7
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("Single.mTEC.Transcriptomes")):
Installation
To install this package, start R (version "3.5") 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. | R Script | |
| Reference Manual |
Details
| biocViews | ExperimentData |
| Version | 1.8.0 |
| License | LGPL |
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| Imports | |
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See More
| Suggests | DESeq2, GenomicRanges, GenomicFeatures, genefilter, statmod, gdata, RColorBrewer, ggplot2, gplots, cluster, clue, grid, gridExtra, ggbio, Gviz, geneplotter, matrixStats, pheatmap, BiocStyle, knitr |
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| Depends On Me | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Single.mTEC.Transcriptomes_1.8.0.tar.gz |
| Windows Binary | |
| Mac OS X 10.11 (El Capitan) | |
| 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 |