Files in jnkoberstein/DEScan
Differential Enrichment Scan
.Rbuildignore
.gitignore
DESCRIPTION
DEScan.Rproj
NAMESPACE
R/count_matrix_functions.R
R/final_region_functions.R
R/peak_call_functions.R
README.md
inst/extdata/Bam/chr19/P43615_Sample_FC1_Input_fwd_chr19_Smartfilter.bam
inst/extdata/Bam/chr19/P43615_Sample_FC1_Input_fwd_chr19_Smartfilter.bam.bai
inst/extdata/Bam/chr19/P43615_Sample_FC4_Input_fwd_chr19_Smartfilter.bam
inst/extdata/Bam/chr19/P43615_Sample_FC4_Input_fwd_chr19_Smartfilter.bam.bai
inst/extdata/Bam/chr19/P43615_Sample_HC1_Input_fwd_chr19_Smartfilter.bam
inst/extdata/Bam/chr19/P43615_Sample_HC1_Input_fwd_chr19_Smartfilter.bam.bai
inst/extdata/Bam/chr19/P43615_Sample_HC4_Input_fwd_chr19_Smartfilter.bam
inst/extdata/Bam/chr19/P43615_Sample_HC4_Input_fwd_chr19_Smartfilter.bam.bai
inst/extdata/Bam/chr19/P43616_Sample_FC6_Input_fwd_chr19_Smartfilter.bam
inst/extdata/Bam/chr19/P43616_Sample_FC6_Input_fwd_chr19_Smartfilter.bam.bai
inst/extdata/Bam/chr19/P43616_Sample_FC9_Input_fwd_chr19_Smartfilter.bam
inst/extdata/Bam/chr19/P43616_Sample_FC9_Input_fwd_chr19_Smartfilter.bam.bai
inst/extdata/Bam/chr19/P43616_Sample_HC6_Input_fwd_chr19_Smartfilter.bam
inst/extdata/Bam/chr19/P43616_Sample_HC6_Input_fwd_chr19_Smartfilter.bam.bai
inst/extdata/Bam/chr19/P43616_Sample_HC9_Input_fwd_chr19_Smartfilter.bam
inst/extdata/Bam/chr19/P43616_Sample_HC9_Input_fwd_chr19_Smartfilter.bam.bai
inst/extdata/Bed/P43615_Sample_FC1_Input_fwd_chr19_Smartfilter.bed.zip
inst/extdata/Bed/P43615_Sample_FC4_Input_fwd_chr19_Smartfilter.bed.zip
inst/extdata/Bed/P43615_Sample_HC1_Input_fwd_chr19_Smartfilter.bed.zip
inst/extdata/Bed/P43615_Sample_HC4_Input_fwd_chr19_Smartfilter.bed.zip
inst/extdata/Bed/P43616_Sample_FC6_Input_fwd_chr19_Smartfilter.bed.zip
inst/extdata/Bed/P43616_Sample_FC9_Input_fwd_chr19_Smartfilter.bed.zip
inst/extdata/Bed/P43616_Sample_HC6_Input_fwd_chr19_Smartfilter.bed.zip
inst/extdata/Bed/P43616_Sample_HC9_Input_fwd_chr19_Smartfilter.bed.zip
inst/extdata/Peaks/chr19/Peaks_P43615_Sample_FC1_Input_fwd_chr19_Smartfilter.RData
inst/extdata/Peaks/chr19/Peaks_P43615_Sample_FC4_Input_fwd_chr19_Smartfilter.RData
inst/extdata/Peaks/chr19/Peaks_P43615_Sample_HC1_Input_fwd_chr19_Smartfilter.RData
inst/extdata/Peaks/chr19/Peaks_P43615_Sample_HC4_Input_fwd_chr19_Smartfilter.RData
inst/extdata/Peaks/chr19/Peaks_P43616_Sample_FC6_Input_fwd_chr19_Smartfilter.RData
inst/extdata/Peaks/chr19/Peaks_P43616_Sample_FC9_Input_fwd_chr19_Smartfilter.RData
inst/extdata/Peaks/chr19/Peaks_P43616_Sample_HC6_Input_fwd_chr19_Smartfilter.RData
inst/extdata/Peaks/chr19/Peaks_P43616_Sample_HC9_Input_fwd_chr19_Smartfilter.RData
inst/extdata/Regions/FinalRegions_allChr.bed
man/catRegions.Rd
man/countFinalRegions.Rd
man/finalRegions.Rd
man/findPeaks.Rd
man/get_disjoint_max_win.Rd
man/loadPeaks.Rd
man/make_grid.Rd
man/merge_overlapping_intervals.Rd
man/read_bam.Rd
man/window_coverage.Rd
testData/Bed/chr19/P43615_Sample_FC1_Input_fwd_chr19_Smartfilter.bed.zip
testData/Bed/chr19/P43615_Sample_FC4_Input_fwd_chr19_Smartfilter.bed.zip
testData/Bed/chr19/P43615_Sample_HC1_Input_fwd_chr19_Smartfilter.bed.zip
testData/Bed/chr19/P43615_Sample_HC4_Input_fwd_chr19_Smartfilter.bed.zip
testData/Bed/chr19/P43616_Sample_FC6_Input_fwd_chr19_Smartfilter.bed.zip
testData/Bed/chr19/P43616_Sample_FC9_Input_fwd_chr19_Smartfilter.bed.zip
testData/Bed/chr19/P43616_Sample_HC6_Input_fwd_chr19_Smartfilter.bed.zip
testData/Bed/chr19/P43616_Sample_HC9_Input_fwd_chr19_Smartfilter.bed.zip
testData/FinalRegions/FinalRegions_chr19.bed
testData/Peaks/chr19/Peaks_P43615_Sample_FC1_Input_fwd_chr19_Smartfilter.RData
testData/Peaks/chr19/Peaks_P43615_Sample_FC4_Input_fwd_chr19_Smartfilter.RData
testData/Peaks/chr19/Peaks_P43615_Sample_HC1_Input_fwd_chr19_Smartfilter.RData
testData/Peaks/chr19/Peaks_P43615_Sample_HC4_Input_fwd_chr19_Smartfilter.RData
testData/Peaks/chr19/Peaks_P43616_Sample_FC6_Input_fwd_chr19_Smartfilter.RData
testData/Peaks/chr19/Peaks_P43616_Sample_FC9_Input_fwd_chr19_Smartfilter.RData
testData/Peaks/chr19/Peaks_P43616_Sample_HC6_Input_fwd_chr19_Smartfilter.RData
testData/Peaks/chr19/Peaks_P43616_Sample_HC9_Input_fwd_chr19_Smartfilter.RData
testData/bams/P43615_Sample_FC1_Input_fwd_chr19_Smartfilter.bam
testData/bams/P43615_Sample_FC1_Input_fwd_chr19_Smartfilter.bam.bai
testData/bams/P43615_Sample_FC4_Input_fwd_chr19_Smartfilter.bam
testData/bams/P43615_Sample_FC4_Input_fwd_chr19_Smartfilter.bam.bai
testData/bams/P43615_Sample_HC1_Input_fwd_chr19_Smartfilter.bam
testData/bams/P43615_Sample_HC1_Input_fwd_chr19_Smartfilter.bam.bai
testData/bams/P43615_Sample_HC4_Input_fwd_chr19_Smartfilter.bam
testData/bams/P43615_Sample_HC4_Input_fwd_chr19_Smartfilter.bam.bai
testData/bams/P43616_Sample_FC6_Input_fwd_chr19_Smartfilter.bam
testData/bams/P43616_Sample_FC6_Input_fwd_chr19_Smartfilter.bam.bai
testData/bams/P43616_Sample_FC9_Input_fwd_chr19_Smartfilter.bam
testData/bams/P43616_Sample_FC9_Input_fwd_chr19_Smartfilter.bam.bai
testData/bams/P43616_Sample_HC6_Input_fwd_chr19_Smartfilter.bam
testData/bams/P43616_Sample_HC6_Input_fwd_chr19_Smartfilter.bam.bai
testData/bams/P43616_Sample_HC9_Input_fwd_chr19_Smartfilter.bam
testData/bams/P43616_Sample_HC9_Input_fwd_chr19_Smartfilter.bam.bai
testData/countmatrix.txt
tests/testthat.R
tests/testthat/bam_peaks.rds
tests/testthat/bed_peaks.rds
tests/testthat/final_regions.rds
tests/testthat/testPeaks.R
tests/testthat/testRegions.R
vignettes/DEScan.Rmd
vignettes/DEScan.pdf
vignettes/DEScan_files/figure-html/rawPlot-1.png
vignettes/DEScan_files/figure-html/rawPlot-2.png
vignettes/DEScan_files/figure-html/ruvPlot-1.png
vignettes/DEScan_files/figure-html/ruvPlot-2.png
vignettes/DEScan_files/figure-latex/rawPlot-1.pdf
vignettes/DEScan_files/figure-latex/rawPlot-2.pdf
vignettes/DEScan_files/figure-latex/ruvPlot-1.pdf
vignettes/DEScan_files/figure-latex/ruvPlot-2.pdf
vignettes/FinalRegions/FinalRegions_chr19.bed
vignettes/countmatrix.txt
