TarSeqQC

This package is for version 3.14 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see TarSeqQC.

TARgeted SEQuencing Experiment Quality Control

DOI: 10.18129/B9.bioc.TarSeqQC

Bioconductor version: 3.14

The package allows the representation of targeted experiment in R. This is based on current packages and incorporates functions to do a quality control over this kind of experiments and a fast exploration of the sequenced regions. An xlsx file is generated as output.

Author: Gabriela A. Merino, Cristobal Fresno, Yanina Murua, Andrea S. Llera and Elmer A. Fernandez

Maintainer: Gabriela Merino <merino.gabriela33 at gmail.com>

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

Installation

To install this package, start R (version "4.1") and enter:


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

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("TarSeqQC")

TarSeqQC: Targeted Sequencing Experiment Quality Control PDF R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alignment, Coverage, DataImport, QualityControl, Sequencing, Software, TargetedResequencing, Visualization

Version 1.24.0

In Bioconductor since BioC 3.2 (R-3.2) (8.5 years)

License GPL (>=2)

Depends R (>= 3.5.1), methods, GenomicRanges, Rsamtools(>= 1.9.2), ggplot2, plyr, openxlsx

Imports grDevices, stats, utils, S4Vectors, IRanges, BiocGenerics, reshape2, GenomeInfoDb, BiocParallel, Biostrings, cowplot, graphics, GenomicAlignments, Hmisc

System Requirements

URL http://www.bdmg.com.ar

Suggests BiocManager, RUnit

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 TarSeqQC_1.24.0.tar.gz

Windows Binary TarSeqQC_1.24.0.zip

macOS 10.13 (High Sierra) TarSeqQC_1.24.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/TarSeqQC

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TarSeqQC

Bioc Package Browser https://code.bioconductor.org/browse/TarSeqQC/

Package Short Url https://bioconductor.org/packages/TarSeqQC/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.14 Source Archive