parathyroidSE

DOI: 10.18129/B9.bioc.parathyroidSE    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see parathyroidSE.

RangedSummarizedExperiment for RNA-Seq of primary cultures of parathyroid tumors by Haglund et al., J Clin Endocrinol Metab 2012.

Bioconductor version: 3.7

This package provides RangedSummarizedExperiment objects of read counts in genes and exonic parts for paired-end RNA-Seq data from experiments on primary cultures of parathyroid tumors. The data were presented in the article "Evidence of a Functional Estrogen Receptor in Parathyroid Adenomas" by Haglund F, Ma R, Huss M, Sulaiman L, Lu M, Nilsson IL, Hoog A, Juhlin CC, Hartman J, Larsson C, J Clin Endocrinol Metab. jc.2012-2484, Epub 2012 Sep 28, PMID: 23024189. The sequencing was performed on tumor cultures from 4 patients at 2 time points over 3 conditions (DPN, OHT and control). One control sample was omitted by the paper authors due to low quality. The package vignette describes the creation of the object from raw sequencing data provided by NCBI Gene Expression Omnibus under accession number GSE37211. The gene and exon features are the GRCh37 Ensembl annotations.

Author: Michael Love

Maintainer: Michael Love <michaelisaiahlove at gmail.com>

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("parathyroidSE")

 

PDF	R Script	parathyroidGenesSE
PDF		Reference Manual

Details

biocViews	ExperimentData, RNASeqData, SequencingData
Version	1.18.0
License	LGPL
Depends	SummarizedExperiment, R (>= 2.10)
Imports
LinkingTo
Suggests	Rsamtools, GenomicAlignments, GEOquery, SRAdb, GenomicFeatures, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me	ClassifyR, DEXSeq, simulatorZ
Links To Me
Build Report

Package Archives

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

Source Package	parathyroidSE_1.18.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
Source Repository	git clone https://git.bioconductor.org/packages/parathyroidSE
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/parathyroidSE
Package Short Url	http://bioconductor.org/packages/parathyroidSE/
Package Downloads Report	Download Stats