6d66814db73a0b526dcd39f019df67d4 *DESCRIPTION
b3931321f3db1763fe074aff675f3d87 *NAMESPACE
1b52ac56738eddcb76e632cee5ef8319 *NEWS.md
c5dbc6dae438b669d9c33231a1c3f7f5 *R/EpiCompare.R
32f5ef95ee15c3525f139a68904a8f1e *R/as_interactive.R
065b5d7672200796ceb8d59abe406aac *R/bpplapply.R
ce302ea01654d622ec52e0ab471bb67b *R/checkCache.R
23253dcd52855c58287a248313b19365 *R/check_cell_lines.R
e29087468c7f44d238737604ad6c0c08 *R/check_dep.R
0348065326cff7bc9cb88fa78e07891b *R/check_genome_build.R
f987ac789793d91da9eca37677ff2dbf *R/check_grlist_cols.R
dc5e722b461c2cf720b80b798ec58117 *R/check_heatmap_args.R
0dc34ccea4e6db9d82fed86cf3748230 *R/check_list_names.R
1487a33ee1b5bdc9277d8a67f0eb95b5 *R/check_peakfiles.R
4b87682ff394a2435c4cbe081ef71cc7 *R/check_unused_args.R
829fa32473f5ace804f6f91903bb95dc *R/check_workers.R
dbaa8485e0cae53cb581abc7da4ae8fa *R/clean_granges.R
b056bdf59a0dabe729056f14450b50d7 *R/compute_consensus_peaks.R
0ef12e0568dc2ceeba6aa23d02434c3b *R/compute_consensus_peaks_consensusseeker.R
ba624b31fd95ca0f5a796cde200e4715 *R/compute_consensus_peaks_granges.R
76aee42b44b847b4b0ea7e0b377ed586 *R/compute_corr.R
4b6b377c0524fad52e08340a9a2ffc4a *R/compute_percentiles.R
4ca5b0f481e16c8353133d4b6cc7c0d2 *R/data.R
a7213be0450aaf5efe7aaeeb365b1e0d *R/download_button.R
ca2bce4ef455f0dfda3ac0b32c6032df *R/fig_length.R
5794fe2ac917ca5982127427835c2696 *R/filter_percentiles.R
c8f7917a7f2f275a56b1d302a248991c *R/fragment_info.R
00be22ef02305a3bb801ec6a51c88f19 *R/gather_files.R
e1b04eda0aa9286ba9127c94e35c3b91 *R/gather_files_names.R
dd896923f6a6dd11a9b7ebb09a9c756c *R/get_bpparam.R
654e2e9bf39cb7e3f674b53ca90f9d40 *R/get_chain_file.R
d9f7fe96b788d88a0b9377f4606885f4 *R/get_chromHMM_annotation.R
8246e622de3c38d45b22cb3c65f176e2 *R/get_pkg_data.R
4865506a191436ba480e08aed3cbf6a4 *R/group_files.R
afcc63b9c82e8de74aa3fb4ca880f4f4 *R/heatmap_heatmaply.R
61a7bc3fc5ee8450e54ba6bd54d57103 *R/heatmap_plotly.R
bfaf06732d5f116a4c4ebf2d7c06155d *R/is_granges.R
8426273afe5b2cd33bb8efc828147f8c *R/liftover_grlist.R
eae1318e1a4c86aafde8581faf6cfb2c *R/message_parallel.R
4a07007e1d643cb47176cb9f3348cbe4 *R/messager.R
65f7b33676f7829d3d50d39bc28938f6 *R/overlap_heatmap.R
f98efa96b1049b9cef6b2ce53f6dc3f9 *R/overlap_percent.R
baa57cebf84b968c6bff039c602d73a5 *R/overlap_stat_plot.R
011edad7bdf897f88cac299f7f848467 *R/overlap_upset_plot.R
c52f78dc15e53b78c14ebf87e6decbfe *R/peak_info.R
43dc890386a6d0920375ccce319e9d00 *R/plot_ChIPseeker_annotation.R
88fae4df7a93fdd0718114d4375bca0c *R/plot_chromHMM.R
005656b618e742c9e30239bd7a8e9145 *R/plot_corr.R
32a9c062709ba5ab93500c3dc0c9f09c *R/plot_enrichment.R
d65ae9e645f0a52fb4ec684981988076 *R/plot_precision_recall.R
2fe2afe5f065a3c8ca5093b3d47a67b0 *R/plot_precision_recall_f1.R
970369094f07f895c4b8ee3c67af6e97 *R/plot_precision_recall_prcurve.R
c854703e5dad4b4e1a50cec75d977fa1 *R/precision_recall.R
563391d11fbae24a5b994536d5cb174c *R/precision_recall_matrix.R
f8648b4d95112d5a38ae7be876336e33 *R/predict_precision_recall.R
156f57ff8427d27aaf377286427601c9 *R/predict_values.R
87166fd7f5275ccb314563235d4a749d *R/prepare_blacklist.R
b4c10836d805cb1c11722009d8b08665 *R/prepare_genome_builds.R
73ee2b65d29feffcf3a03006916e614b *R/prepare_output_build.R
37aaed0c758d8e498fc976034eab2dce *R/prepare_peaklist.R
3e655826a2eea6a033aa15b8f82a2fcc *R/prepare_reference.R
ce921c87939cb69ed0a60e3f072f495c *R/read_bam.R
9e87d47cedebc8341c026aa1385c0517 *R/read_bowtie.R
b822bda73948a4409c07568a49809569 *R/read_multiqc.R
b6fa3de1217b1c2e470063446b3246ad *R/read_peaks.R
aec24f51ab189303c8ae41d62c07886f *R/read_picard.R
66865ca2bdbe549f218e56669b174b1d *R/read_trimgalore.R
fdbc363240714b83e82dcfaec1607b6a *R/rebin_peaks.R
71588876d3c43dce468974ec01417b0b *R/remove_empty_elements.R
5a92181eb99ea9ec727af48159df12f5 *R/remove_nonstandard_chrom.R
2fd69f36f1e0f1f0556eefae8495e7b5 *R/report_command.R
237ff023f1a7f2c0421d71423bdb827f *R/report_header.R
91afde7d32b37060303267c837df92bd *R/report_time.R
026573017ade9e48b2135b3fa02c6d96 *R/save_output.R
55c4ee217452c28ff1db8bb75ed1ab95 *R/save_results.R
9dc10ba799a73cf5fbf100628ce2e701 *R/set_min_max.R
908bf243c447a6e03faa916f4fcb5e73 *R/stopper.R
5ab66c4e5a9ac128a09ad05896877f52 *R/tidy_chromosomes.R
c82f2eb315c68050cce8771ef8a34428 *R/tidy_peakfile.R
3a82e15e9c7c69b3a84fd65723baa265 *R/translate_genome.R
ac79792770547397839c16d149af578d *R/tss_plot.R
e7efe66cebdfe135e9917a059c130144 *R/width_boxplot.R
9a0973482d53bca2993ca943f40765bd *R/write_example_peaks.R
59eef382a0bc5f5bb4a3b38b3f159146 *README.md
125d5131ad80f3e44ae1c86a649085cf *build/vignette.rds
f06acc556520e8806d1b9ead215e4cae *data/CnR_H3K27ac.rda
506d45a4121db3436b2626876a171c0e *data/CnR_H3K27ac_picard.rda
4b2d3c470c34c5c4cb1d2a103373070b *data/CnT_H3K27ac.rda
c756db9b0b6a5f7ebb2899be857b1d9b *data/CnT_H3K27ac_picard.rda
5a79a6a2904e95ca8e9f0435a61be0f0 *data/encode_H3K27ac.rda
bb396c33c8c8678193da02a7c4eeba62 *data/hg19_blacklist.rda
dfe76cdde44a347457bb25bbb3de6e0f *data/hg38_blacklist.rda
4de0a172aeec7e9a4a36227fee03c5a5 *data/mm10_blacklist.rda
82826c60b1150d7faa8c9bed2926e25f *data/mm9_blacklist.rda
fb9de602d6866a9f94fd990c0b3f8655 *inst/CITATION
52af5040036b0b1fe70c9dd3c4c03b17 *inst/doc/EpiCompare.R
9e43d9bee82f8ee28405c884af072e5a *inst/doc/EpiCompare.Rmd
4a870608cd20bca079cfae3b58a48f32 *inst/doc/EpiCompare.html
9a72ccb8a91618db17d05c51327b451e *inst/doc/docker.R
b6bb76e66807aa292173677b492a4e62 *inst/doc/docker.Rmd
5020b800d59e0c2994a1841f29907a16 *inst/doc/docker.html
6f2a8a4be71765e79d14147625604a07 *inst/doc/example_report.R
5d5cf953456f89e9afbad357ee40eb56 *inst/doc/example_report.Rmd
9afdd2f956453f1cce7a824cac996ec2 *inst/doc/example_report.html
38b031c17613232e6797e8209fdedd11 *inst/hex/genetic_scale.png
4e75aa46ae26e1b45687e1412c43086f *inst/hex/hex.png
830d943f0592c52477e7eebd0bc9caee *inst/hex/hexSticker.Rmd
891147943c107f6408e257d1e0c76ccf *inst/markdown/EpiCompare.Rmd
a62bcdbeec9a7effb5ed28f6758f86c5 *inst/markdown/custom.css
34dceaa71d09d709c3161f82497e847c *man/CnR_H3K27ac.Rd
8bff7b321ec029ab0f882bdd894909be *man/CnR_H3K27ac_picard.Rd
b3bfdb59450095918017f346556e18d9 *man/CnT_H3K27ac.Rd
a9799b2e3e01ecbf5f6bf4d2f55503ac *man/CnT_H3K27ac_picard.Rd
301f74b4f15c38017815a55add5cb001 *man/EpiCompare.Rd
808e7abc6799049087a1bcbae0f88835 *man/as_interactive.Rd
6c9e9a4a98674833d634256e5c0be97a *man/bpplapply.Rd
6f13c93dc1168ade457b6f15f1a419b9 *man/checkCache.Rd
f859623bfd4ab92a4209ca9bbd1beab1 *man/check_cell_lines.Rd
2249e10ec1f5aeff7f0c86739893dacc *man/check_genome_build.Rd
2a99468b7028ce517ab5ebad43f4491b *man/check_grlist_cols.Rd
07bc1cc7690d42d62bd962038f77856c *man/check_list_names.Rd
1687dade1fd749a15651951a0585930e *man/check_workers.Rd
a4d04af45fb4ec279a47f31f7682770f *man/clean_granges.Rd
7260a5445a0d53310ab425ba777f259e *man/compute_consensus_peaks.Rd
00414749431ef5f6a95d48fd06766160 *man/compute_corr.Rd
aa4cd7c727661b06f9a9e23b1f5d8f8a *man/download_button.Rd
3a317263084d0b8f1af5e52d0821bb06 *man/encode_H3K27ac.Rd
64b444e994a2c7449e8d968d6b46cccb *man/fig_length.Rd
1b66b0f5ee33111e17b82ed11530a63f *man/fragment_info.Rd
f09452712fbb593881982b3423b28da9 *man/gather_files.Rd
40c85cf79dd743d4fcb68814b56a1d34 *man/gather_files_names.Rd
7b39162aa2aff3450ce7cc4349d99426 *man/get_bpparam.Rd
6f76a745dac07a3e21ca5fe9a0d8a73e *man/get_chromHMM_annotation.Rd
2b16c40cd53a1f3840e60d055d4ef030 *man/group_files.Rd
0a17dba2d5f27cefec5728db7df7eb22 *man/hg19_blacklist.Rd
c9e02a0f9d053683a670b634a8cdbc15 *man/hg38_blacklist.Rd
7ca579ca288c6bb2ef4c00979fc29ab5 *man/is_granges.Rd
9ce37cfdb3fabd10c9a04884d2a7d421 *man/liftover_grlist.Rd
e90f74cc4df95de300f2fc2496df0e03 *man/message_parallel.Rd
e9f58180ea3cfa511d9da3a24986f10e *man/messager.Rd
70818aa9b1f0fe978e2ac7b3efb58f5d *man/mm10_blacklist.Rd
ab6b94184a4f24db9d52b70d4dc594c5 *man/mm9_blacklist.Rd
af831d25dea94ec9131c00d0128be3e1 *man/overlap_heatmap.Rd
e109d0dee5354d2d80e19e0276fee0cc *man/overlap_percent.Rd
0cf1ef91546ada923be34966911564f0 *man/overlap_stat_plot.Rd
2c9049230139ce77d9e5636a7d1a52dd *man/overlap_upset_plot.Rd
79a852ca325816a430321142e789b579 *man/peak_info.Rd
464ec1767527adb8501dd58d53ca02ef *man/plot_ChIPseeker_annotation.Rd
78693190ab2ca8b710030ecff4d00343 *man/plot_chromHMM.Rd
9230b5aed977f3d6b804d476c908dd5d *man/plot_corr.Rd
3bbd173c7d0947b349e1a4a003d7b48d *man/plot_enrichment.Rd
abb2cb5aecc46604bfbdf93a1fc84b94 *man/plot_precision_recall.Rd
4e55ec127985cced1a4995eda6d0597a *man/precision_recall.Rd
10c764ed0648693a728b61a4d9f24994 *man/precision_recall_matrix.Rd
f73a86440e0275415fd2550bc9251a29 *man/predict_precision_recall.Rd
ab13a07dfc62967ef01e19a759d3b259 *man/predict_values.Rd
1172dcb6dd1283a1a6c26c8b1d5ddfe9 *man/prepare_blacklist.Rd
5999855e607d3896bb1fa68fc4f3fb22 *man/prepare_genome_builds.Rd
01b20ad66c6214a98d9c3562e08d4aca *man/prepare_peaklist.Rd
55c3f8b614e8cefcb2f879f4af6ce82b *man/prepare_reference.Rd
33baa17e001283916cadef365029a9cf *man/read_bowtie.Rd
d6c3d4b2eb77bb5a973c9fc20dbf0b33 *man/read_peaks.Rd
aceb6b2136379ee2def712bedd2f7847 *man/rebin_peaks.Rd
09d3470452c54fd42e973748f01602ce *man/remove_nonstandard_chrom.Rd
6ae9f2105e4a641aac3a9f8f17bb2e62 *man/report_command.Rd
c121804f56da300b5813ad65fc700cce *man/report_header.Rd
54eda09daecdba2db9becd7c74c7127e *man/save_output.Rd
c0610b3e9074b00213ce2eb09d486ef3 *man/set_min_max.Rd
108d27f24c6980606447ed2ab5793b01 *man/stopper.Rd
d086c04c78ac4d0539ff6dcd4bab576c *man/tidy_chromosomes.Rd
c80ba24c3d1284ea29b22d14cc43fc44 *man/tidy_peakfile.Rd
8f813d998deb3e743ecaf6c8612f27e4 *man/translate_genome.Rd
e8a01ed76ca6a8f371182172710b478f *man/tss_plot.Rd
822699dfc33a69e9e3c177a8097d243a *man/width_boxplot.Rd
9cad4055538d4172782648203e19d038 *man/write_example_peaks.Rd
4df0ec3b27a8def274c08d6953b402ca *tests/test.Rmd
a1cf4e21dbf0c285cc308c25f8525bdc *tests/test.html
6101521c89c14e59b790ec1e70563fb0 *tests/testthat.R
368ab63b3489af970a960583c8304f6f *tests/testthat/test-EpiCompare.R
1ed573a2af372d468f884c1ea2ceedd6 *tests/testthat/test-bpplapply.R
0bc0f202d62832676b62400271513964 *tests/testthat/test-compute_consensus_peaks.R
890626645dd62ac231a5ea3cab1087dc *tests/testthat/test-compute_corr.R
ec594858d1ad50bf9421792eb91a7989 *tests/testthat/test-fragment_info.R
fc075f94ab9890025ffb87b1ed31bce6 *tests/testthat/test-gather_files.R
d8286e9f822c88963dd3e59caed912b1 *tests/testthat/test-group_files.R
43ce63845b23608b747fb1cc79fd78aa *tests/testthat/test-import_narrowPeak.R
6fc3107b72ac8abc3a1b79bbc6808db2 *tests/testthat/test-input_peakfile_prep.R
c9195729a52b650b4f2dd9df74d79926 *tests/testthat/test-liftover_grlist.R
e69e97873b7b0db7473bf49b7dd42fa3 *tests/testthat/test-output_files.R
ca9d84e0b1aed0b6771c1fb0f5df58ab *tests/testthat/test-overlap_heatmap.R
d7849eeeda5caa0d38409cd2c59d3696 *tests/testthat/test-overlap_stat_plot.R
99ba3c82e6da03fe7816a2346240abf3 *tests/testthat/test-peak_info.R
ca51c0df8ea553200566fcee2433708c *tests/testthat/test-plot_corr.R
513de6cb260d5277ae73caf6aa7b3289 *tests/testthat/test-plot_precision_recall.R
b4933184665a4347001081c6b993884b *tests/testthat/test-rebin_peaks.R
53ff84b5d528312d0aad79a97f2fcbf9 *tests/testthat/test-report_header.R
2a43a423252d71b5e83528fb606aaede *tests/testthat/test-tidy_chromosomes.R
8caf069d2f3a07d71427bcf0ab1e8859 *tests/testthat/test-tss_plot.R
4fa683ad36fa7f1fab53c35aa054a7da *tests/testthat/test-width_boxplot.R
9e43d9bee82f8ee28405c884af072e5a *vignettes/EpiCompare.Rmd
b6bb76e66807aa292173677b492a4e62 *vignettes/docker.Rmd
5d5cf953456f89e9afbad357ee40eb56 *vignettes/example_report.Rmd
