ampliQueso: Analysis of amplicon enrichment panels
Version 1.14.0

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

Browse man pages Browse package API and functions Browse package files

AuthorAlicja Szabelska <alicja.szabelska@up.poznan.pl>; Marek Wiewiorka <marek.wiewiorka@gmail.com>; Michal Okoniewski <michal@fgcz.ethz.ch>
Bioconductor views DifferentialExpression GeneExpression RNASeq ReportWriting Sequencing Transcription Visualization
Date of publicationNone
MaintainerMichal Okoniewski <michal@fgcz.ethz.ch>
LicenseGPL-2
Version1.14.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ampliQueso")

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

Functions

aveSimpleSamples Source code
ave_varSamples Source code
averageSamples Source code
callCamelTestReg Source code
callCompareCoverages Source code
callCompareCoveragesBatch Source code
callSamPileup Source code
camelSampleTable Man page
camelTest Man page Source code Source code
camelTestParReg Source code
compareCoverages Man page Source code
compareCoveragesReg Man page Source code
compareCoveragesRegApply Source code
compareCoveragesRegParM Source code
compareCoveragesRegParR Source code
compareCoveragesRegSeq Source code
diff_stat Source code
escSpecialChars Source code
getCountTable Man page Source code
getSNP Man page Source code Source code
getSNPPar Source code
getSNPSamples Source code
loadLibs Source code
localMax Source code
ndMax Man page
ndMin Man page
perm.samples Source code
rs2Counts Source code
runAQReport Man page Source code
setdiff.data.frame Source code
shuffle Source code
strand2number Source code

Files

DESCRIPTION
NAMESPACE
R
R/auxFunctions.R
R/compareCoverages.R
R/compareCoveragesRegions.R
R/getCamelTests.R
R/getCountTable.R
R/getSNP.R
R/runAQReport.R
build
build/vignette.rds
data
data/ampliQueso.RData
inst
inst/NEWS
inst/doc
inst/doc/ampliQueso.R
inst/doc/ampliQueso.Rnw
inst/doc/ampliQueso.pdf
inst/extdata
inst/extdata/AQ.bed
inst/extdata/covdesc
inst/extdata/sample_033_sort.bam
inst/extdata/sample_033_sort.bam.bai
inst/extdata/sample_034_sort.bam
inst/extdata/sample_034_sort.bam.bai
inst/extdata/sample_035_sort.bam
inst/extdata/sample_035_sort.bam.bai
inst/extdata/sample_036_sort.bam
inst/extdata/sample_036_sort.bam.bai
inst/extdata/sample_043_sort.bam
inst/extdata/sample_043_sort.bam.bai
inst/extdata/sample_044_sort.bam
inst/extdata/sample_044_sort.bam.bai
inst/extdata/sample_045_sort.bam
inst/extdata/sample_045_sort.bam.bai
inst/extdata/sample_046_sort.bam
inst/extdata/sample_046_sort.bam.bai
inst/figure
inst/figure/cheese-icon.png
inst/reports
inst/reports/aq_article.Rnw
inst/reports/aq_beamer.Rnw
inst/reports/aq_html.Rhtml
man
man/camelSampleTable.Rd
man/camelTest.Rd
man/compareCoverages.Rd
man/compareCoveragesReg.Rd
man/getCountTable.Rd
man/getSNP.Rd
man/ndMax.Rd
man/ndMin.Rd
man/runAQReport.Rd
vignettes
vignettes/ampliQueso.Rnw
vignettes/fig1.png
ampliQueso documentation built on May 20, 2017, 10:07 p.m.