Files in DAMEfinder

Finds DAMEs - Differential Allelicly MEthylated regions

README.md

NAMESPACE

DESCRIPTION

LICENSE

build/vignette.rds

data/extractbams_output.rda

data/readtuples_output.rda

R/simes_pval.R R/get_tstats.R R/methyl_MDS_plot.R R/calc_asm.R R/median_tracks.R R/methyl_circle_plot.R R/empirical_pval.R R/split_bams.R R/calc_derivedasm.R R/read_tuples.R R/score_tracks.R R/data.R R/split_reads.R R/DAMEfinder-package.R R/find_dames.R vignettes/DAMEfinder_workflow.Rmd

vignettes/papers.bib

man/dame_track_mean.Rd man/dame_track.Rd man/calc_asm.Rd man/getMD.Rd man/empirical_pval.Rd man/calc_derivedasm.Rd man/calc_score.Rd man/read_tuples.Rd man/get_tstats.Rd man/calc_weight.Rd man/extractbams_output.Rd man/simes_pval.Rd man/DAMEfinder.Rd man/methyl_circle_plotCpG.Rd man/modulus_sqrt.Rd man/readtuples_output.Rd man/find_dames.Rd man/methyl_MDS_plot.Rd man/calc_logodds.Rd man/methyl_circle_plot.Rd man/splitReads.Rd man/extract_bams.Rd tests/testthat.R tests/testthat/test-dame_track.R tests/testthat/test-split_bams.R tests/testthat/test-dame_track_median.R tests/testthat/test-split_reads.R tests/testthat/test-methyl_circle_plot.R tests/testthat/test-mdsplot.R tests/testthat/test-tupleasm_dames.R tests/testthat/test-derivedasm_dames.R

inst/NEWS.Rd

inst/CITATION

inst/doc/DAMEfinder_workflow.R

inst/doc/DAMEfinder_workflow.html

inst/doc/DAMEfinder_workflow.Rmd

inst/extdata/CRC1_chr19_trim.bam.bai

inst/extdata/CRC1.chr19.trim.vcf

inst/extdata/NORM1_chr19.qs.CG.2.tsv.gz

inst/extdata/NORM1_chr19_trim.bam

inst/extdata/NORM1.chr19.trim.vcf

inst/extdata/NORM1_chr19_trim.bam.bai

inst/extdata/CRC1_chr19_trim.bam

inst/extdata/CRC1_chr19.qs.CG.2.tsv.gz

inst/figures/DAMEfinder_workflow.png

inst/figures/DAME_only30reads.png

inst/figures/DAME_tuple_allsamps.png

inst/figures/DAME_snp_allsamps.png

inst/figures/DAME_snp_sampledreads.png

inst/figures/DAME_tuple_allsamps_median.png

inst/figures/DAME_snp_allsamps_median.png

inst/figures/damefindersticker.png

inst/scripts/file_description.txt

inst/scripts/readtuples_output.R inst/scripts/extractbams_output.R

DAMEfinder documentation built on Nov. 8, 2020, 11:10 p.m.