Files in BBCG/epialleleR
Fast, Epiallele-Aware Methylation Caller and Reporter
.github/.gitignore
.github/workflows/check-bioc.yml
.gitignore
DESCRIPTION
NAMESPACE
NEWS
R/RcppExports.R
R/callMethylation.R
R/extractPatterns.R
R/generateBedEcdf.R
R/generateBedReport.R
R/generateCytosineReport.R
R/generateMhlReport.R
R/generateVcfReport.R
R/internal.R
R/plotPatterns.R
R/preprocessBam.R
R/preprocessGenome.R
R/simulateBam.R
README.md
_pkgdown.yml
inst/CITATION
inst/extdata/amplicon.bed
inst/extdata/amplicon.vcf.gz
inst/extdata/amplicon.vcf.gz.tbi
inst/extdata/amplicon000meth.bam
inst/extdata/amplicon010meth.bam
inst/extdata/amplicon100meth.bam
inst/extdata/capture.bam
inst/extdata/capture.bed
inst/extdata/capture.vcf.gz
inst/extdata/capture.vcf.gz.tbi
inst/extdata/test/bsmap-pe-namesort-zs.bam
inst/extdata/test/bsmap-pe-unsort-zs.bam
inst/extdata/test/bsmap-se-unsort-zs.bam
inst/extdata/test/bwameth-pe-namesort-yd.bam
inst/extdata/test/bwameth-pe-unsort-yd.bam
inst/extdata/test/bwameth-se-unsort-yd.bam
inst/extdata/test/bwameth-se-unsort.bam
inst/extdata/test/dragen-pe-namesort-xg-xm.bam
inst/extdata/test/dragen-pe-namesort-xg.bam
inst/extdata/test/dragen-pe-unsort-xg-xm.bam
inst/extdata/test/dragen-pe-unsort-xg.bam
inst/extdata/test/dragen-pe.CX_report.txt.gz
inst/extdata/test/dragen-se-unsort-xg-xm.bam
inst/extdata/test/dragen-se-unsort-xg.bam
inst/extdata/test/dragen-se.CX_report.txt.gz
inst/extdata/test/empty.bam
inst/extdata/test/reference.fasta.gz
inst/extdata/test/reference.fasta.gz.fai
inst/extdata/test/reference.fasta.gz.gzi
inst/unitTests/test_callMethylation.R
inst/unitTests/test_extractPatterns.R
inst/unitTests/test_generateBedEcdf.R
inst/unitTests/test_generateBedReport.R
inst/unitTests/test_generateCytosineReport.R
inst/unitTests/test_generateMhlReport.R
inst/unitTests/test_generateVcfReport.R
inst/unitTests/test_internals.R
inst/unitTests/test_plotPatterns.R
inst/unitTests/test_preprocessBam.R
inst/unitTests/test_preprocessGenome.R
inst/unitTests/test_simulateBam.R
man/callMethylation.Rd
man/extractPatterns.Rd
man/generateBedEcdf.Rd
man/generateBedReport.Rd
man/generateCytosineReport.Rd
man/generateMhlReport.Rd
man/generateVcfReport.Rd
man/plotPatterns.Rd
man/preprocessBam.Rd
man/preprocessGenome.Rd
man/simulateBam.Rd
src/.gitignore
src/Makevars
src/RcppExports.cpp
src/epialleleR.h
src/rcpp_call_methylation.cpp
src/rcpp_check_bam.cpp
src/rcpp_cx_report.cpp
src/rcpp_extract_patterns.cpp
src/rcpp_fep.cpp
src/rcpp_get_base_freqs.cpp
src/rcpp_get_xm_beta.cpp
src/rcpp_match_target.cpp
src/rcpp_mhl_report.cpp
src/rcpp_read_bam.cpp
src/rcpp_read_genome.cpp
src/rcpp_simulate_bam.cpp
src/rcpp_threshold_reads.cpp
tests/runTests.R
vignettes/epialleleR.Rmd
vignettes/epialleleR_logo.svg
vignettes/epialleles.png
vignettes/values.Rmd
