ampliQueso: Analysis of amplicon enrichment panels

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The package provides tools and reports for the analysis of amplicon sequencing panels, such as AmpliSeq

Author
Alicja Szabelska <alicja.szabelska@up.poznan.pl>; Marek Wiewiorka <marek.wiewiorka@gmail.com>; Michal Okoniewski <michal@fgcz.ethz.ch>
Date of publication
None
Maintainer
Michal Okoniewski <michal@fgcz.ethz.ch>
License
GPL-2
Version
1.12.0

View on Bioconductor

Man pages

camelSampleTable
ampliQueso sample data
camelTest
camelTest - calculating permutation tests for camel measures...
compareCoverages
compareCoverages - camel measure for a single comparison.
compareCoveragesReg
compareCoveragesReg - calculating given camel measures for a...
getCountTable
getCountTable - obtaining typical count table.
getSNP
getSNP - finding SNPs in all samples for regions specified by...
ndMax
ampliQueso sample data
ndMin
ampliQueso sample data
runAQReport
runAQReport - runing the AmpliQueso report

Files in this package

ampliQueso/DESCRIPTION
ampliQueso/NAMESPACE
ampliQueso/R
ampliQueso/R/auxFunctions.R
ampliQueso/R/compareCoverages.R
ampliQueso/R/compareCoveragesRegions.R
ampliQueso/R/getCamelTests.R
ampliQueso/R/getCountTable.R
ampliQueso/R/getSNP.R
ampliQueso/R/runAQReport.R
ampliQueso/build
ampliQueso/build/vignette.rds
ampliQueso/data
ampliQueso/data/ampliQueso.RData
ampliQueso/inst
ampliQueso/inst/NEWS
ampliQueso/inst/doc
ampliQueso/inst/doc/ampliQueso.R
ampliQueso/inst/doc/ampliQueso.Rnw
ampliQueso/inst/doc/ampliQueso.pdf
ampliQueso/inst/extdata
ampliQueso/inst/extdata/AQ.bed
ampliQueso/inst/extdata/covdesc
ampliQueso/inst/extdata/sample_033_sort.bam
ampliQueso/inst/extdata/sample_033_sort.bam.bai
ampliQueso/inst/extdata/sample_034_sort.bam
ampliQueso/inst/extdata/sample_034_sort.bam.bai
ampliQueso/inst/extdata/sample_035_sort.bam
ampliQueso/inst/extdata/sample_035_sort.bam.bai
ampliQueso/inst/extdata/sample_036_sort.bam
ampliQueso/inst/extdata/sample_036_sort.bam.bai
ampliQueso/inst/extdata/sample_043_sort.bam
ampliQueso/inst/extdata/sample_043_sort.bam.bai
ampliQueso/inst/extdata/sample_044_sort.bam
ampliQueso/inst/extdata/sample_044_sort.bam.bai
ampliQueso/inst/extdata/sample_045_sort.bam
ampliQueso/inst/extdata/sample_045_sort.bam.bai
ampliQueso/inst/extdata/sample_046_sort.bam
ampliQueso/inst/extdata/sample_046_sort.bam.bai
ampliQueso/inst/figure
ampliQueso/inst/figure/cheese-icon.png
ampliQueso/inst/reports
ampliQueso/inst/reports/aq_article.Rnw
ampliQueso/inst/reports/aq_beamer.Rnw
ampliQueso/inst/reports/aq_html.Rhtml
ampliQueso/man
ampliQueso/man/camelSampleTable.Rd
ampliQueso/man/camelTest.Rd
ampliQueso/man/compareCoverages.Rd
ampliQueso/man/compareCoveragesReg.Rd
ampliQueso/man/getCountTable.Rd
ampliQueso/man/getSNP.Rd
ampliQueso/man/ndMax.Rd
ampliQueso/man/ndMin.Rd
ampliQueso/man/runAQReport.Rd
ampliQueso/vignettes
ampliQueso/vignettes/ampliQueso.Rnw
ampliQueso/vignettes/fig1.png