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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("TEQC")
AuthorM. Hummel, S. Bonnin, E. Lowy, G. Roma
Bioconductor views Genetics Microarray QualityControl Sequencing
Date of publicationNone
MaintainerManuela Hummel <m.hummel@dkfz.de>
LicenseGPL (>= 2)
Version3.16.0

View on Bioconductor

Functions

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

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.