Package: TEQC 4.34.0

Sarah Bonnin

TEQC: Quality control for target capture experiments

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.

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

TEQC_4.34.0.tar.gz
TEQC_4.34.0.zip(r-4.7)TEQC_4.34.0.zip(r-4.6)TEQC_4.34.0.zip(r-4.5)
TEQC_4.34.0.tgz(r-4.6-any)TEQC_4.34.0.tgz(r-4.5-any)
TEQC_4.34.0.tar.gz(r-4.7-any)TEQC_4.34.0.tar.gz(r-4.6-any)
TEQC_4.34.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
TEQC/json (API)
NEWS

# Install 'TEQC' in R:

install.packages('TEQC', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:TEQC-4.35.0(bioc 3.24)TEQC-4.34.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

qualitycontrol microarray sequencing genetics

4.48 score 8 scripts 421 downloads 17 mentions 22 exports 23 dependencies

Last updated from:cfaf74a039 (on RELEASE_3_23). Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	ERROR	161
linux-devel-x86_64	WARNING	260
source / vignettes	OK	221
linux-release-x86_64	WARNING	198
macos-release-arm64	WARNING	136
macos-oldrel-arm64	WARNING	125
windows-devel	WARNING	144
windows-release	WARNING	157
windows-oldrel	WARNING	163
wasm-release	OK	122

Exports:chrom.barplot coverage.correlation coverage.density coverage.GC coverage.hist coverage.plot coverage.target coverage.targetlength.plot coverage.uniformity covered.k duplicates.barplot fraction.reads.target fraction.target get.baits get.reads get.targets insert.size.hist make.wigfiles multiTEQCreport reads2pairs readsPerTarget TEQCreport

Dependencies:BH Biobase BiocGenerics BiocParallel Biostrings bitops codetools cpp11 crayon formatR futile.logger futile.options generics GenomicRanges hwriter IRanges lambda.r Rhtslib Rsamtools S4Vectors Seqinfo snow XVector

TEQC

Rendered fromTEQC.Rnwusingutils::Sweaveon May 30 2026.

Last update: 2020-09-10
Started: 2013-11-01

Help page	Topics
Reads per chromosome barplot	chrom.barplot
Coverage correlation plot	coverage.correlation
Coverage density plot	coverage.density
Bait coverage versus GC content plot	coverage.GC
Coverage histogram	coverage.hist
Coverage versus base position plot	coverage.plot
Calculates read coverage	coverage.target
Number of reads or average coverage versus target length scatter plot	coverage.targetlength.plot
Coverage uniformity plot	coverage.uniformity
Target capture sensitivity	covered.k
Read duplicates barplot	duplicates.barplot
Target capture specificity	fraction.reads.target
Fraction of the target within the genome	fraction.target
Read capture hybridization probe positions	get.baits
Read genomic positions of sequencing data	get.reads
Read capture target positions	get.targets
Insert sizes histogram	insert.size.hist
Creates wiggle files with per-base coverages	make.wigfiles
Creates an html report for multiple samples	multiTEQCreport
Merges reads to read pairs	reads2pairs
Numbers of reads per target	readsPerTarget
Creates an html report	TEQCreport

Package: TEQC 4.34.0

TEQC: Quality control for target capture experiments

TEQC

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)