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.

AuthorM. Hummel, S. Bonnin, E. Lowy, G. Roma
Date of publicationNone
MaintainerManuela Hummel <m.hummel@dkfz.de>
LicenseGPL (>= 2)
Version3.14.0

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

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

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