Files in AllenInstitute/lowcat
Low Coverage Accessibility and Transcriptomics
.Rbuildignore
.gitignore
CONTRIBUTING.md
DESCRIPTION
LICENSE
NAMESPACE
R/distances.R
R/genomic_ranges.R
R/io_and_formats.R
R/parallelization.R
R/plotting_functions.R
R/transcription_functions.R
R/ucsc_functions.R
R/util.R
R/xx_deprecated.R
inst/testdata/bam/N702-N504_S13_L001_R1_001.rmd.srt.bam
inst/testdata/bam/N702-N506_S15_L001_R1_001.rmd.srt.bam
inst/testdata/bam/N702-N507_S16_L001_R1_001.rmd.srt.bam
inst/testdata/build_testdata.R
inst/testdata/rda/simple_regions.rda
lowcat.Rproj
man/GRanges_to_bed.Rd
man/GRanges_to_ucsc_loc.Rd
man/all_column_correlation.Rd
man/balance_fragment_clusters.Rd
man/bam_to_fragment_list.Rd
man/bed_to_GRanges.Rd
man/bed_to_ucsc_loc.Rd
man/build_pile_heatmap.Rd
man/build_pile_plot.Rd
man/cat_update.Rd
man/clusterApplyLB_chunks.Rd
man/collapse_fragment_list.Rd
man/combine_group_GRanges.Rd
man/compare_fragment_lists.Rd
man/convert_fragment_list.Rd
man/count_fragment_overlaps.Rd
man/downsample_fragments.Rd
man/expand_fragments.Rd
man/filter_fragments.Rd
man/fragments_to_windows.Rd
man/get_gene_bodies.Rd
man/get_great_regions.Rd
man/get_tss_regions.Rd
man/hello.Rd
man/matrix_var_filter.Rd
man/max_column_correlation.Rd
man/merge_bam_files.Rd
man/overlap_jaccard_df.Rd
man/overlap_jaccard_df_fun.Rd
man/overlap_jaccard_mat.Rd
man/overlap_jaccard_mat_fun.Rd
man/pe_to_frag.Rd
man/pe_to_frag_parallel.Rd
man/percent_display.Rd
man/pileup_gr_list.Rd
man/read_multiplexed_paired_bam.Rd
man/region_fragment_count.Rd
man/res_to_distance_matrix.Rd
man/run_fragment_overlap_jaccard_parallel.Rd
man/run_fragment_overlap_jaccard_parallel_full.Rd
man/run_pe_to_frag_parallel.Rd
man/run_se_to_cuts_parallel.Rd
man/run_window_overlap_jaccard_parallel.Rd
man/se_to_cuts.Rd
man/se_to_cuts_parallel.Rd
man/time_display.Rd
man/ucsc_loc_to_GRanges.Rd
man/ucsc_loc_to_bed.Rd
man/window_jaccard_df.Rd
man/window_jaccard_df_fun.Rd
readme.md
tests/testthat.R
tests/testthat/test-region_manipulation.R
