Files in SamBuckberry/RunATAC
Functions for Importing, Processing, Analyzing, Plotting and Reformatting ATAC-seq Data
.DS_Store
.Rbuildignore
.gitignore
DESCRIPTION
LICENCE
NAMESPACE
R/bam_to_centres_bigwig.R
R/bam_to_insertions_bigwig.R
R/calc_dinuc_freq.R
R/calc_frip.R
R/calc_ins_bias.R
R/calc_ins_pwm.R
R/calc_motif_dist.R
R/calc_profile_bias.R
R/calc_v.R
R/motif_gr.R
R/plot_insert_size.R
R/plot_scaled_footprint.R
R/plot_v.R
R/range_summary.R
R/read_atac_frags.R
R/read_atac_insertions.R
R/read_bed.R
R/write_functions.R
README.Rmd
README.md
README_files/figure-html/unnamed-chunk-13-1.png
README_files/figure-html/unnamed-chunk-3-1.png
README_files/figure-markdown_github/unnamed-chunk-13-1.png
README_files/figure-markdown_github/unnamed-chunk-15-1.png
README_files/figure-markdown_github/unnamed-chunk-3-1.png
README_files/figure-markdown_github/unnamed-chunk-9-1.png
RunATAC.Rproj
TODO.Rmd
TODO.md
data/.DS_Store
inst/.DS_Store
inst/extdata/chrIV.bam
inst/extdata/chrIV.bam.bai
inst/extdata/chrIV.ins.bigwig
inst/extdata/chrIV.nuc.bigwig
inst/extdata/chrIV_peaks.narrowPeak
inst/extdata/ctcf.pwm
man/bam_to_centres_bw.Rd
man/bam_to_insertions_bw.Rd
man/calc_dinuc_freq.Rd
man/calc_frip.Rd
man/calc_ins_bias.Rd
man/calc_ins_pwm.Rd
man/calc_motif_dist.Rd
man/calc_v.Rd
man/motif_gr.Rd
man/plot_insert_size.Rd
man/plot_scaled_footprint.Rd
man/plot_v.Rd
man/range_summary.Rd
man/read_atac_frags.Rd
man/read_atac_insertions.Rd
man/read_bed.Rd
man/write_gr_bed.Rd
man/write_insertions_bw.Rd
man/write_nuc_bw.Rd
map_atac_pe.sh
testing/atac_footprinting.R
testing/bam_to_offset_bed.R
testing/call_atac_peaks.R
testing/centipede_footprinting.R
testing/normalise_atac_footprints.R
testing/plot_bias_corrected_footprint.R
testing/plot_footprint.R
tests/testthat/test_plots.R
tests/testthat/test_ranges.R
