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

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

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