Single.mTEC.Transcriptomes

This is the released version of Single.mTEC.Transcriptomes; for the devel version, see Single.mTEC.Transcriptomes.

Single Cell Transcriptome Data and Analysis of Mouse mTEC cells

Bioconductor version: Release (3.23)

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")):

Seminal Bioconductor project articles:

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.

Installation

To install this package, start R (version "4.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ExperimentData
Version	1.40.0
License	LGPL
Depends	R (>= 3.5.0)
Imports
System Requirements
URL

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
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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_1.40.0.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-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