Rariant: Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies
Version 1.12.0

The 'Rariant' package identifies single nucleotide variants from sequencing data based on the difference of binomially distributed mismatch rates between matched samples.

Browse man pages Browse package API and functions Browse package files

AuthorJulian Gehring, Simon Anders, Bernd Klaus
Bioconductor views GenomicVariation Sequencing SomaticMutation StatisticalMethod VariantDetection Visualization
Date of publicationNone
MaintainerJulian Gehring <jg-bioc@gmx.com>
LicenseGPL-3
Version1.12.0
URL https://github.com/juliangehring/Rariant
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Rariant")

Man pages

ci-adjust: CI Adjust
ci-assessment: Assessment of CI methods
ci-utils: CI Utils
colorscales: Rariant color scales
convert-utils: Position converters
evidence-heatmap: Variant Evidence Heatmap
mismatch-plot: Mismatch plot from BAM files
mismatch-utils: Tally processing low-level functions
multi-utils: Multi call processing
plot-cis: Plotting Functions
prop-cis: Confidence Interval Functions
prop-tests: Testing Functions
rariant: Rariant calling functions
Rariant-package: Rariant package
shiny: Interactive inspection
split-sample: Split Sample for Binomial Data
tally: Tally a genomic region
yesnomaybe: Determine Variant Evidence

Functions

Rariant Man page
Rariant-package Man page
acCi Man page Source code
acCi4 Source code
baseFillScale Man page Source code
binGRanges Source code
binomTestPval Source code
blogit Source code
callConsensus Man page Source code
call_base Source code
checkCalls Source code
ciAdjustLevel Man page Source code
ciCovers Man page Source code
ciOutside Man page Source code
ciOverlap Man page Source code
ciWidth Man page Source code
classifyEvent Source code
combineCalls Source code
comparativeMismatch Source code
coverageProbability Man page Source code
df2gr Source code
dna_bases Source code
ds2int Source code
eventFillScale Man page Source code
evidenceHeatmap Man page Source code
exampleCalls Source code
feTest Man page Source code
filterCalls Man page Source code
findCalls Man page Source code
gr2df Source code
gr2pos Man page Source code
gr2vr Source code
grDensity Source code
ind2base Source code
mat2ind Source code
mergeCalls Man page Source code
mismatchCount Man page Source code
mismatchUtils Man page
nhsCi Man page Source code
nmTest Man page Source code
nmTestOld Source code
plotAbundanceShift Man page Source code
plotCIs Man page
plotConfidenceIntervals Man page Source code
plotRates Source code
plotShiftSupport Source code
pos2gr Man page Source code
propCIs Man page
propTests Man page
rariant Man page
rariant,BamFile,BamFile,GRanges-method Man page
rariant,array,array,GRanges-method Man page
rariant,character,character,GRanges-method Man page
rariant-methods Man page
rariantFromBam Source code
rariantFromMatrix Source code
rariantInspect Man page Source code
rariantStandalone Man page Source code
rateFillScale Man page Source code
rdSimulate Source code
readRariant Man page Source code
reevalSites Source code
scoreTest Man page Source code
selectStrand Man page Source code
seqDepth Man page Source code
splitSample Man page
splitSampleBinom Man page Source code
str_capture_matrix Source code
tallyBamRegion Man page Source code
tallyPlot Man page Source code
updateCalls Man page Source code
verdictColorScale Man page Source code
vr2gr Source code
wilsonScore Source code
writeRariant Man page Source code
yesNoMaybe Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/blogit.R
R/ci-adjust.R
R/ci-utils.R
R/ci.R
R/colorscales.R
R/convert.R
R/coverage-probs.R
R/examples.R
R/mismatch-plot.R
R/multi-plot.R
R/multi-stat.R
R/multi-utils.R
R/plot.R
R/rariant-highlevel.R
R/rariant-methods.R
R/rariant-standalone.R
R/rariantFromBam.R
R/rariantFromMatrix.R
R/shiny.R
R/split.R
R/stats.R
R/tally.R
R/tests.R
R/utils.R
build
build/vignette.rds
inst
inst/doc
inst/doc/Rariant-vignette.R
inst/doc/Rariant-vignette.Rhtml
inst/doc/Rariant-vignette.html
inst/doc/rariant-inspect-ci.png
inst/doc/rariant-inspect-shift.png
inst/extdata
inst/extdata/platinum
inst/extdata/platinum/control.bam
inst/extdata/platinum/control.bam.bai
inst/extdata/platinum/mix.bam
inst/extdata/platinum/mix.bam.bai
inst/extdata/platinum/test.bam
inst/extdata/platinum/test.bam.bai
inst/extdata/platinum/test2.bam
inst/extdata/platinum/test2.bam.bai
inst/scripts
inst/scripts/platinum-sim.sh
inst/scripts/rariant
inst/tests
inst/tests/test-ci-functions.R
inst/tests/test-rariant-highlevel.R
inst/tests/test-rariant-methods-1kg.R
inst/tests/test-tally.R
man
man/Rariant-package.rd
man/ci-adjust.rd
man/ci-assessment.rd
man/ci-utils.rd
man/colorscales.rd
man/convert-utils.rd
man/evidence-heatmap.rd
man/mismatch-plot.rd
man/mismatch-utils.rd
man/multi-utils.rd
man/plot-cis.rd
man/prop-cis.rd
man/prop-tests.rd
man/rariant.rd
man/shiny.rd
man/split-sample.rd
man/tally.rd
man/yesnomaybe.rd
tests
tests/test_all.R
vignettes
vignettes/Rariant-vignette.Rhtml
vignettes/Rariant-vignette.org
vignettes/bioc.css
vignettes/references.bib
vignettes/references.html
Rariant documentation built on May 20, 2017, 9:20 p.m.