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TEQC (version 3.12.0)

Quality control for target capture experiments

Description

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.

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Version

Version

3.12.0

License

GPL (>= 2)

Maintainer

Manuela Hummel

Last Published

February 15th, 2017

Functions in TEQC (3.12.0)

coverage.density

Coverage density plot
fraction.reads.target

Target capture specificity
readsPerTarget

Numbers of reads per target
chrom.barplot

Reads per chromosome barplot
duplicates.barplot

Read duplicates barplot
get.baits

Read capture hybridization probe positions
reads2pairs

Merges reads to read pairs
coverage.uniformity

Coverage uniformity plot
coverage.hist

Coverage histogram
get.reads

Read genomic positions of sequencing data
coverage.plot

Coverage versus base position plot
fraction.target

Fraction of the target within the genome
coverage.targetlength.plot

Number of reads or average coverage versus target length scatter plot
TEQCreport

Creates an html report
insert.size.hist

Insert sizes histogram
get.targets

Read capture target positions
coverage.correlation

Coverage correlation plot
coverage.target

Calculates read coverage
multiTEQCreport

Creates an html report for multiple samples
coverage.GC

Bait coverage versus GC content plot
make.wigfiles

Creates wiggle files with per-base coverages
covered.k

Target capture sensitivity