TEQC: Quality control for target capture experiments

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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
Date of publication
None
Maintainer
Manuela Hummel <m.hummel@dkfz.de>
License
GPL (>= 2)
Version
3.14.0

View on Bioconductor

Man pages

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

Files in this package

TEQC/DESCRIPTION
TEQC/NAMESPACE
TEQC/NEWS
TEQC/R
TEQC/R/TEQCreport.R
TEQC/R/chrom.barplot.R
TEQC/R/coverage.GC.R
TEQC/R/coverage.correlation.R
TEQC/R/coverage.density.R
TEQC/R/coverage.hist.R
TEQC/R/coverage.plot.R
TEQC/R/coverage.target.R
TEQC/R/coverage.targetlength.plot.R
TEQC/R/coverage.uniformity.R
TEQC/R/covered.k.R
TEQC/R/duplicates.barplot.R
TEQC/R/fraction.reads.target.R
TEQC/R/fraction.target.R
TEQC/R/get.baits.R
TEQC/R/get.reads.R
TEQC/R/get.targets.R
TEQC/R/insert.size.hist.R
TEQC/R/make.wigfiles.R
TEQC/R/multiTEQCreport.R
TEQC/R/myreduce.R
TEQC/R/offsetfun.R
TEQC/R/reads2pairs.R
TEQC/R/readsPerTarget.R
TEQC/R/zzz.R
TEQC/build
TEQC/build/vignette.rds
TEQC/inst
TEQC/inst/CITATION
TEQC/inst/doc
TEQC/inst/doc/TEQC.R
TEQC/inst/doc/TEQC.Rnw
TEQC/inst/doc/TEQC.pdf
TEQC/inst/extdata
TEQC/inst/extdata/ExampleSet_Baits.txt
TEQC/inst/extdata/ExampleSet_Reads.bed
TEQC/inst/extdata/ExampleSet_Targets.bed
TEQC/inst/template
TEQC/inst/template/0000-Header.html
TEQC/inst/template/1000-Overview.html
TEQC/inst/template/1001-Pairedend.html
TEQC/inst/template/2000-SpeciEnrichment.html
TEQC/inst/template/2001-SpeciEnrichment.html
TEQC/inst/template/3000-Coverage.html
TEQC/inst/template/4000-CoverageUniformity.html
TEQC/inst/template/5000-CoverageLength.html
TEQC/inst/template/6000-CoverageGC.html
TEQC/inst/template/7000-Wiggle.html
TEQC/inst/template/8000-Duplicates.html
TEQC/inst/template/8001-Duplicates.html
TEQC/inst/template/9999-Footer.html
TEQC/inst/template/QA.css
TEQC/inst/template/image
TEQC/inst/template/image/bioclogo-small.jpg
TEQC/inst/templateMulti
TEQC/inst/templateMulti/0000-Header.html
TEQC/inst/templateMulti/1000-Overview.html
TEQC/inst/templateMulti/2000-Specificity.html
TEQC/inst/templateMulti/3000-TargetCoverage.html
TEQC/inst/templateMulti/4000-Sensitivity.html
TEQC/inst/templateMulti/5000-Uniformity.html
TEQC/inst/templateMulti/6000-Correlation.html
TEQC/inst/templateMulti/9999-Footer.html
TEQC/man
TEQC/man/TEQCreport.Rd
TEQC/man/chrom.barplot.Rd
TEQC/man/coverage.GC.Rd
TEQC/man/coverage.correlation.Rd
TEQC/man/coverage.density.Rd
TEQC/man/coverage.hist.Rd
TEQC/man/coverage.plot.Rd
TEQC/man/coverage.target.Rd
TEQC/man/coverage.targetlength.plot.Rd
TEQC/man/coverage.uniformity.Rd
TEQC/man/covered.k.Rd
TEQC/man/duplicates.barplot.Rd
TEQC/man/fraction.reads.target.Rd
TEQC/man/fraction.target.Rd
TEQC/man/get.baits.Rd
TEQC/man/get.reads.Rd
TEQC/man/get.targets.Rd
TEQC/man/insert.size.hist.Rd
TEQC/man/make.wigfiles.Rd
TEQC/man/multiTEQCreport.Rd
TEQC/man/reads2pairs.Rd
TEQC/man/readsPerTarget.Rd
TEQC/vignettes
TEQC/vignettes/TEQC.Rnw