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Showing content from https://www.bioconductor.org/packages/devel/data/experiment/html/Single.mTEC.Transcriptomes.html below:

Bioconductor - Single.mTEC.Transcriptomes (development version)

Single.mTEC.Transcriptomes

This is the development version of Single.mTEC.Transcriptomes; for the stable release version, see Single.mTEC.Transcriptomes.

Single Cell Transcriptome Data and Analysis of Mouse mTEC cells

Bioconductor version: Development (3.22)

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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Details biocViews ExperimentData Version 1.37.0 License LGPL Depends R (>= 3.5.0) Imports System Requirements URL See More Suggests DESeq2, GenomicRanges, GenomicFeatures, genefilter, statmod, gdata, RColorBrewer, ggplot2, gplots, cluster, clue, grid, gridExtra, ggbio, Gviz, geneplotter, matrixStats, pheatmap, BiocStyle, knitr, BiocParallel Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

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


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