seqc

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see seqc.

RNA-seq data generated from SEQC (MAQC-III) study

Bioconductor version: 3.9

The SEQC/MAQC-III Consortium has produced benchmark RNA-seq data for the assessment of RNA sequencing technologies and data analysis methods (Nat Biotechnol, 2014). Billions of sequence reads have been generated from ten different sequencing sites. This package contains the summarized read count data for ~2000 sequencing libraries. It also includes all the exon-exon junctions discovered from the study. TaqMan RT-PCR data for ~1000 genes and ERCC spike-in sequence data are included in this package as well.

Author: Yang Liao and Wei Shi with contributions from Gordon K Smyth and Steve Lianoglou.

Maintainer: Yang Liao <liao at wehi.edu.au> and Wei Shi <shi at wehi.edu.au>

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

Installation

To install this package, start R (version "3.6") and enter:


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

BiocManager::install("seqc")

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("seqc")

SEQC Vignette	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ExperimentData, RNASeqData, SequencingData, qPCRData
Version	1.18.0
License	GPL-3
Depends	R (>= 2.10)
Imports	utils, Biobase
System Requirements
URL	http://bioconductor.org/packages/release/data/experiment/html/seqc.html

Suggests
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.

Source Package	seqc_1.18.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
Source Repository	git clone https://git.bioconductor.org/packages/seqc
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/seqc
Package Short Url	https://bioconductor.org/packages/seqc/
Package Downloads Report	Download Stats