Files in neurogenomics/EpiCompare

Comparison, Benchmarking & QC of Epigenomic Datasets

.Rbuildignore

.github/.gitignore

.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature_request.md

.github/workflows/rworkflows.yml

.gitignore

DESCRIPTION

NAMESPACE

NEWS.md R/EpiCompare.R R/as_interactive.R R/bpplapply.R R/checkCache.R R/check_cell_lines.R R/check_dep.R R/check_genome_build.R R/check_grlist_cols.R R/check_heatmap_args.R R/check_list_names.R R/check_unused_args.R R/check_workers.R R/clean_granges.R R/compute_consensus_peaks.R R/compute_consensus_peaks_consensusseeker.R R/compute_consensus_peaks_granges.R R/compute_corr.R R/compute_percentiles.R R/data.R R/download_button.R R/fig_length.R R/filter_percentiles.R R/fragment_info.R R/gather_files.R R/gather_files_names.R R/get_bpparam.R R/get_chain_file.R R/get_chromHMM_annotation.R R/get_pkg_data.R R/group_files.R R/heatmap_heatmaply.R R/heatmap_plotly.R R/is_granges.R R/liftover_grlist.R R/message_parallel.R R/messager.R R/overlap_heatmap.R R/overlap_percent.R R/overlap_stat_plot.R R/overlap_upset_plot.R R/peak_info.R R/plot_ChIPseeker_annotation.R R/plot_chromHMM.R R/plot_corr.R R/plot_enrichment.R R/plot_precision_recall.R R/plot_precision_recall_f1.R R/plot_precision_recall_prcurve.R R/precision_recall.R R/precision_recall_matrix.R R/predict_precision_recall.R R/predict_values.R R/prepare_blacklist.R R/prepare_genome_builds.R R/prepare_output_build.R R/prepare_peaklist.R R/prepare_reference.R R/read_bam.R R/read_bowtie.R R/read_multiqc.R R/read_peaks.R R/read_picard.R R/read_trimgalore.R R/rebin_peaks.R R/remove_empty_elements.R R/remove_nonstandard_chrom.R R/report_command.R R/report_header.R R/report_time.R R/save_output.R R/save_results.R R/set_min_max.R R/stopper.R R/tidy_peakfile.R R/translate_genome.R R/tss_plot.R R/width_boxplot.R R/write_example_peaks.R README.Rmd README.md

data/CnR_H3K27ac.rda

data/CnR_H3K27ac_picard.rda

data/CnT_H3K27ac.rda

data/CnT_H3K27ac_picard.rda

data/encode_H3K27ac.rda

data/hg19_blacklist.rda

data/hg38_blacklist.rda

data/mm10_blacklist.rda

data/mm9_blacklist.rda

inst/CITATION

inst/hex/genetic_scale.png

inst/hex/hex.png

inst/hex/hexSticker.Rmd inst/markdown/EpiCompare.Rmd

inst/markdown/custom.css

man/CnR_H3K27ac.Rd man/CnR_H3K27ac_picard.Rd man/CnT_H3K27ac.Rd man/CnT_H3K27ac_picard.Rd man/EpiCompare.Rd man/as_interactive.Rd man/bpplapply.Rd man/checkCache.Rd man/check_cell_lines.Rd man/check_genome_build.Rd man/check_grlist_cols.Rd man/check_list_names.Rd man/check_workers.Rd man/clean_granges.Rd man/compute_consensus_peaks.Rd man/compute_corr.Rd man/download_button.Rd man/encode_H3K27ac.Rd man/fig_length.Rd man/fragment_info.Rd man/gather_files.Rd man/gather_files_names.Rd man/get_bpparam.Rd man/get_chromHMM_annotation.Rd man/group_files.Rd man/hg19_blacklist.Rd man/hg38_blacklist.Rd man/is_granges.Rd man/liftover_grlist.Rd man/message_parallel.Rd man/messager.Rd man/mm10_blacklist.Rd man/mm9_blacklist.Rd man/overlap_heatmap.Rd man/overlap_percent.Rd man/overlap_stat_plot.Rd man/overlap_upset_plot.Rd man/peak_info.Rd man/plot_ChIPseeker_annotation.Rd man/plot_chromHMM.Rd man/plot_corr.Rd man/plot_enrichment.Rd man/plot_precision_recall.Rd man/precision_recall.Rd man/precision_recall_matrix.Rd man/predict_precision_recall.Rd man/predict_values.Rd man/prepare_blacklist.Rd man/prepare_genome_builds.Rd man/prepare_peaklist.Rd man/prepare_reference.Rd man/read_bowtie.Rd man/read_peaks.Rd man/rebin_peaks.Rd man/remove_nonstandard_chrom.Rd man/report_command.Rd man/report_header.Rd man/save_output.Rd man/set_min_max.Rd man/stopper.Rd man/tidy_peakfile.Rd man/translate_genome.Rd man/tss_plot.Rd man/width_boxplot.Rd man/write_example_peaks.Rd tests/test.Rmd

tests/test.html

tests/testthat.R tests/testthat/test-EpiCompare.R tests/testthat/test-bpplapply.R tests/testthat/test-compute_consensus_peaks.R tests/testthat/test-compute_corr.R tests/testthat/test-fragment_info.R tests/testthat/test-gather_files.R tests/testthat/test-group_files.R tests/testthat/test-import_narrowPeak.R tests/testthat/test-input_peakfile_prep.R tests/testthat/test-liftover_grlist.R tests/testthat/test-output_files.R tests/testthat/test-overlap_heatmap.R tests/testthat/test-overlap_stat_plot.R tests/testthat/test-peak_info.R tests/testthat/test-plot_corr.R tests/testthat/test-plot_precision_recall.R tests/testthat/test-rebin_peaks.R tests/testthat/test-report_header.R tests/testthat/test-tss_plot.R tests/testthat/test-width_boxplot.R

vignettes/.gitignore

vignettes/EpiCompare.Rmd vignettes/docker.Rmd vignettes/example_report.Rmd

neurogenomics/EpiCompare documentation built on April 30, 2024, 3:58 p.m.