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parathyroidSE

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


Bioconductor version: Release (3.18)

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>

Citation (from within R, enter citation("parathyroidSE")):

Installation

To install this package, start R (version "4.3") and enter:


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

BiocManager::install("parathyroidSE")

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("parathyroidSE")
parathyroidGenesSE PDF R Script
Reference Manual PDF

Details

biocViews ExperimentData, RNASeqData, SequencingData
Version 1.40.0
License LGPL
Depends R (>= 3.5.0), SummarizedExperiment
Imports
System Requirements
URL
See More
Suggests Rsamtools, GenomicAlignments, GEOquery, SRAdb, GenomicFeatures, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me ClassifyR, DEXSeq
Links To Me
Build Report Build Report

Package Archives

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

Source Package parathyroidSE_1.40.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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 https://bioconductor.org/packages/parathyroidSE/
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