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TEQC

This is the development version of TEQC; for the stable release version, see TEQC.

Quality control for target capture experiments


Bioconductor version: Development (3.19)

Target capture experiments combine hybridization-based (in solution or on microarrays) capture and enrichment of genomic regions of interest (e.g. the exome) with high throughput sequencing of the captured DNA fragments. This package provides functionalities for assessing and visualizing the quality of the target enrichment process, like specificity and sensitivity of the capture, per-target read coverage and so on.

Author: M. Hummel, S. Bonnin, E. Lowy, G. Roma

Maintainer: Sarah Bonnin <Sarah.Bonnin at crg.eu>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("TEQC")

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("TEQC")
TEQC PDF R Script
Reference Manual PDF

Details

biocViews Genetics, Microarray, QualityControl, Sequencing, Software
Version 4.25.0
In Bioconductor since BioC 2.8 (R-2.13) (13 years)
License GPL (>= 2)
Depends methods, BiocGenerics(>= 0.1.0), IRanges(>= 1.13.5), Rsamtools, hwriter
Imports Biobase(>= 2.15.1)
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Package Archives

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

Source Package TEQC_4.25.0.tar.gz
Windows Binary
macOS Binary (x86_64) TEQC_4.25.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/TEQC
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TEQC
Bioc Package Browser https://code.bioconductor.org/browse/TEQC/
Package Short Url https://bioconductor.org/packages/TEQC/
Package Downloads Report Download Stats