Files in markrobinsonuzh/DAMEfinder
Finds DAMEs - Differential Allelicly MEthylated regions
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/DAMEfinder-package.R
R/calc_asm.R
R/calc_derivedasm.R
R/data.R
R/empirical_pval.R
R/find_dames.R
R/get_tstats.R
R/median_tracks.R
R/methyl_MDS_plot.R
R/methyl_circle_plot.R
R/read_tuples.R
R/score_tracks.R
R/simes_pval.R
R/split_bams.R
R/split_reads.R
README.md
data/extractbams_output.rda
data/readtuples_output.rda
inst/CITATION
inst/NEWS.Rd
inst/extdata/CRC1.chr19.trim.vcf
inst/extdata/CRC1_chr19.qs.CG.2.tsv.gz
inst/extdata/CRC1_chr19_trim.bam
inst/extdata/CRC1_chr19_trim.bam.bai
inst/extdata/NORM1.chr19.trim.vcf
inst/extdata/NORM1_chr19.qs.CG.2.tsv.gz
inst/extdata/NORM1_chr19_trim.bam
inst/extdata/NORM1_chr19_trim.bam.bai
inst/figures/DAME_only30reads.png
inst/figures/DAME_snp_allsamps.png
inst/figures/DAME_snp_allsamps_median.png
inst/figures/DAME_snp_sampledreads.png
inst/figures/DAME_tuple_allsamps.png
inst/figures/DAME_tuple_allsamps_median.png
inst/figures/DAMEfinder_workflow.png
inst/figures/damefindersticker.png
inst/scripts/extractbams_output.R
inst/scripts/file_description.txt
inst/scripts/readtuples_output.R
man/DAMEfinder.Rd
man/calc_asm.Rd
man/calc_derivedasm.Rd
man/calc_logodds.Rd
man/calc_score.Rd
man/calc_weight.Rd
man/dame_track.Rd
man/dame_track_mean.Rd
man/empirical_pval.Rd
man/extract_bams.Rd
man/extractbams_output.Rd
man/find_dames.Rd
man/getMD.Rd
man/get_tstats.Rd
man/methyl_MDS_plot.Rd
man/methyl_circle_plot.Rd
man/methyl_circle_plotCpG.Rd
man/modulus_sqrt.Rd
man/read_tuples.Rd
man/readtuples_output.Rd
man/simes_pval.Rd
man/splitReads.Rd
tests/testthat.R
tests/testthat/test-dame_track.R
tests/testthat/test-dame_track_median.R
tests/testthat/test-derivedasm_dames.R
tests/testthat/test-mdsplot.R
tests/testthat/test-methyl_circle_plot.R
tests/testthat/test-split_bams.R
tests/testthat/test-split_reads.R
tests/testthat/test-tupleasm_dames.R
vignettes/DAMEfinder_workflow.Rmd
vignettes/papers.bib
