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

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

Author
Julian Gehring, Simon Anders, Bernd Klaus
Date of publication
None
Maintainer
Julian Gehring <jg-bioc@gmx.com>
License
GPL-3
Version
1.10.0
URLs

View on Bioconductor

Files in this package

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