parathyroidSE
This package is for version 3.9 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: 3.9
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("parathyroidSE")):
Installation
To install this package, start R (version "3.6") 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 | R Script | |
| Reference Manual |
Details
| biocViews | ExperimentData, RNASeqData, SequencingData |
| Version | 1.22.0 |
| License | LGPL |
| Depends | SummarizedExperiment, R (>= 2.10) |
| 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, simulatorZ |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | parathyroidSE_1.22.0.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 | https://bioconductor.org/packages/parathyroidSE/ |
| Package Downloads Report | Download Stats |