154eabddcac9610c2ea14c3e20233bfb *DESCRIPTION
9657d121c83f8d5bcf69131c6748e220 *NAMESPACE
b9786ce71419d5199de82d68cf86d31d *NEWS.md
85f22977686f177c125c40ef0428b948 *R/AllClasses.R
ff84b08546873669754eb2abdbee5fe8 *R/AllGenerics.R
eebebea00177641dff5e7014dab11474 *R/Argument_checks.R
e3355fb38dd13f4b199e715714220432 *R/Build_Background.R
2f1b32bf7d47210ddf8dc4ee8a0d1328 *R/Helper_functions.R
36eec2a0f6a90b98578193dd385871aa *R/Promoter_selection.R
1e8db27b018f3f2c0c92bd4fe79956f6 *R/PscanR.R
477153ec92c8183ca10e5e0fa5566567 *R/Scan_and_post_processing.R
4aaf6feda92e93567fc877acacea04b3 *R/Transcript_schemes.R
18ebf494f25467f02a682ea4fdaae325 *R/methods-PSMatrix.R
0c52b8cacdf100b675a1f6b9fd1d241f *README.md
21c9401b8c07f38d762ade4612fc4ffe *build/partial.rdb
74c526f750547f1604baa3bb7018220c *build/vignette.rds
1c4033aae8305c70902178cce85fc39b *inst/CITATION
ce2258e49f19713d092d5c9548f859ac *inst/DATA_SOURCES.md
5c8e661bdd209c6a99a72179207d55b6 *inst/PROVENANCE.md
8e2b5595207fa64c6445cd5f8a1b060e *inst/doc/PscanRQuickOverview.R
12a90fe71d2118194b36dc494a4c92ab *inst/doc/PscanRQuickOverview.Rmd
5f6568c8751e49bb3b5534484970dfef *inst/doc/PscanRQuickOverview.html
b13572bcdf3524ed2b4617ce346465cd *inst/doc/PscanR_Arabidopsis_BPC.R
f4ab76aaa416708c8d941310e10e6e53 *inst/doc/PscanR_Arabidopsis_BPC.Rmd
24406dbb92db950076c222c82177ac10 *inst/doc/PscanR_Arabidopsis_BPC.html
54bd58cd4b044c22289aeeea25b13f6b *inst/doc/PscanR_Custom_Background.R
0e6ed7bc2ebb00d8e9ab07cba6478952 *inst/doc/PscanR_Custom_Background.Rmd
36c02c67b6615034fe21ef6cda22ae22 *inst/doc/PscanR_Custom_Background.html
19b8de756e4403fbbc70b18ead0e8652 *inst/doc/PscanR_Mouse_HD_Retina.R
8eb7e8ecc47e4428b95174b92b55b743 *inst/doc/PscanR_Mouse_HD_Retina.Rmd
3bc8bacae2e429f03def93b526e89c93 *inst/doc/PscanR_Mouse_HD_Retina.html
8a1a22c098a769cec9220990972e1dfc *inst/doc/PscanR_concepts_and_input.R
122590d14db0fd7cd0ba4d15f59662c0 *inst/doc/PscanR_concepts_and_input.Rmd
0fb12a2c38d14179ff3217a890bd5f09 *inst/doc/PscanR_concepts_and_input.html
d82651c2d40807adc44cbd9cd9b1141f *inst/extdata/J2020.rds
55011b5ec526ee15c41909a3bc736bf3 *inst/extdata/J2020_hg38_200u_50d_UCSC.psbg.txt
028453cea916735fb01616be5f46d2a9 *inst/extdata/PscanR_background_catalog_v2.tsv
ac606a2b2ebe9d7a8fc22f7ac8edaf0d *inst/extdata/full_pfm1.rds
3c037f7184f4daeaa7e50cf838c8a989 *inst/extdata/full_pfms.rds
25cd7b7b160ce573d996238f83c32d57 *inst/extdata/nrf1100.txt
341fbc56544c6f932433ea385a2c813a *inst/extdata/pfm1.rds
1d91c37795778e29a20f4edaec581eab *inst/extdata/prom_seq.rds
63c51e85eb3e0f4ef2c451d29fb123dd *inst/extdata/vignettes/arabidopsis_bpc/arabidopsis_bpc_gene_sets.tsv
608f40a0af059ba993a517a4321638b4 *inst/extdata/vignettes/arabidopsis_bpc/arabidopsis_bpc_results.rds
bbb2a3b2897fad6d782b26d3a102503b *inst/extdata/vignettes/arabidopsis_bpc/promoter_selection_example.rds
5a2837153aeb5a00f3a17e09bcab170d *inst/extdata/vignettes/custom_background/J2020_sacCer3_950u_50d_UCSC.rebuild.txt
b99b5b76f55f974591bcfaacd27b67e6 *inst/extdata/vignettes/custom_background/fullbg_motifs.tsv
e9f57fbb93587de8740afa92ee2f5a2a *inst/extdata/vignettes/custom_background/rp_promoters.rds
feda50757d67fefd4189c1298a907dcc *inst/extdata/vignettes/custom_background/sacCer3_950u_50d_fullBG_15motifs.rds
a881a04d11ef480e654c7bb9f532334d *inst/extdata/vignettes/custom_background/timings_1core.tsv
be377aa7331404773b4fd3d0e9ebc449 *inst/extdata/vignettes/custom_background/timings_8core.tsv
74fea98772cb8ed7edb9950d1b039902 *inst/extdata/vignettes/custom_background/ucbg_summary.rds
e901ea0ac9afc83d4792814b5bbf6a54 *inst/extdata/vignettes/mouse_hd_retina/mm10_950u_50d_refseq_snapshot.rds
4f32630dbdec400b021cc35d330c7d38 *inst/extdata/vignettes/mouse_hd_retina/paper_subset_membership.tsv
8acd072ddaac2c9c622f1f88281a77b1 *inst/extdata/vignettes/mouse_hd_retina/promoter_selection_example.rds
a3e0c3a4d7b8af3139711885a56fa1a5 *inst/extdata/vignettes/mouse_hd_retina/uc2_vignette_data.rds
d5fd0c9b1328d3bcd12dfae4d40018ab *inst/scripts/J2020.R
2f66a76e5ec10c52faa2515f6a96b8ee *inst/scripts/J2020_hg38_200u_50d_UCSC_curated.R
4b7e9b0240556d548e5b256b132658dd *inst/scripts/fixture-provenance.md
c02ede656164318acaa35408f55c06e2 *inst/scripts/full_pfm1.R
90d6957a742774bfaf593d91954768e3 *inst/scripts/make-arabidopsis-example.R
1e6977e188b46d38e0b330e5e91d8802 *inst/scripts/pfm1.R
000baa8dda7740caa8626f21ec1a8317 *inst/scripts/prom_seq.R
5ca97d9a63067f8612c45a27c7d3693b *man/PSMatrix.Rd
45be00366a2fb9e140bd2808a5049f3a *man/PSMatrixList.Rd
401466d4272db6fbfb237daec92d99fe *man/PscanR.Rd
8caf59f80af54a044ef2cc3bc9e3e7c9 *man/ps_available_bg.Rd
46202fc40241e3dbbdcd1be04dce7206 *man/ps_bg_avg-PSMatrix-method.Rd
17c1680ad560958179c7589ed7dd5b98 *man/ps_bg_avg-set-PSMatrix-method.Rd
16ab781c968554a536f7e02bbc2acc8f *man/ps_bg_avg-set.Rd
460a8f87f2676be81158e81badf50498 *man/ps_bg_avg.Rd
d99a5f50e41503f88868699d9d3ffcba *man/ps_bg_seq_names-PSMatrix-method.Rd
654dd5816320c69c6f58f011b02dc68a *man/ps_bg_seq_names.Rd
4f9a221bf8dc19c88eed84aa0dbb2935 *man/ps_bg_size-PSMatrix-method.Rd
068ca8c76aa1422f99b13f818a3f36a8 *man/ps_bg_size-set-PSMatrix-method.Rd
98b68809b141ce341ad988ad922a7113 *man/ps_bg_size-set.Rd
641341476970c5dbe1daab5917586ff8 *man/ps_bg_size.Rd
58a2f250c10ff77ca3a3706304b3b3fd *man/ps_bg_std_dev-PSMatrix-method.Rd
fd649bc63bd110687e0136de9b5ee8b3 *man/ps_bg_std_dev-set-PSMatrix-method.Rd
dd817b19e0cf71ed5dd283f7ea8a5f17 *man/ps_bg_std_dev-set.Rd
2c230c2c5ff2ed7f06f0620ccef84c9a *man/ps_bg_std_dev.Rd
4d87492fb192be4d7f6dae67c9b168c1 *man/ps_build_bg.Rd
b1bc0c088ddc83619b65f8cfcc497c05 *man/ps_build_bg_from_table.Rd
90f68583612a64ba347f58d25aa1afc8 *man/ps_density_plot.Rd
f62b62c22aee3e08d2270fe0a7ff9a33 *man/ps_fg_avg-PSMatrix-method.Rd
d93ccd0b5d8eae1bd99f1aa1233c36b8 *man/ps_fg_avg.Rd
dd2ba5a50b47fe214faed0504de657e2 *man/ps_fg_size-PSMatrix-method.Rd
c7ba02fbe6344e0d43705e206294ef30 *man/ps_fg_size.Rd
8ff60e24f9d919128048f28f894c7a9f *man/ps_get_bg_table.Rd
c99e890d16b462be84a27adfea9d39f4 *man/ps_hit_score_plot.Rd
d47bf24443b58aa7efb46e24bba22c32 *man/ps_hitpos_map.Rd
8ff5f51127723e51dff6577a60ef84a5 *man/ps_hits_oligo-PSMatrix-method.Rd
7152f61ec2a878de471c5755945e5296 *man/ps_hits_oligo.Rd
317f3ce9af83945b691dfaee60c2356b *man/ps_hits_oligo_bg-PSMatrix-method.Rd
4696e260164ed5e9192afa6bf1cbb17e *man/ps_hits_oligo_bg.Rd
705c98dcb9177c03973328646b6a8510 *man/ps_hits_pos-PSMatrix-method.Rd
384c885875faa73fd887b28487e1dba5 *man/ps_hits_pos.Rd
2e19c6d180d2883da215d47f4b3b1ac6 *man/ps_hits_pos_bg-PSMatrix-method.Rd
44cc44cfa526ea3635b83560aa63f7fe *man/ps_hits_pos_bg.Rd
c908fa1b82d70f0dfb1f4db6792d5474 *man/ps_hits_score-PSMatrix-method.Rd
f5e4aac4adb24efd6c2e470a5df2c668 *man/ps_hits_score.Rd
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41a61964c1bb601efee789c5ef9c92d1 *man/ps_hits_score_bg.Rd
434172059c581d92dcfb36f99dc83b1b *man/ps_hits_size-PSMatrix-method.Rd
227bc74b858988151fa5e4dcb7913a3c *man/ps_hits_size.Rd
ca928e1a037c82114aa06c87bbf89a88 *man/ps_hits_strand-PSMatrix-method.Rd
e569f67ffbead49c355a00d6182962cd *man/ps_hits_strand.Rd
de9340bdb128f80acadaaefc0401003a *man/ps_hits_strand_bg-PSMatrix-method.Rd
9cf3cf5c045771f864321bd31d7a9ff9 *man/ps_hits_strand_bg.Rd
1a793e8eb710b83f1cacada98296b4ef *man/ps_hits_table-PSMatrix-method.Rd
cce1778d380a1ad489d1d53a53f343b5 *man/ps_hits_table.Rd
ea96d6621d12063d06bf766671b92020 *man/ps_hits_z-PSMatrix-method.Rd
4a4f18d4118a7138e7880e6a23121e7e *man/ps_hits_z.Rd
f2211bcf992e6813fdcd87092a7a9ba7 *man/ps_load_select_transcripts.Rd
5980044f09d801f9081272b56a728073 *man/ps_motif_barplot.Rd
b188c9d3555fd8b6b3e3bb5fa33abcd1 *man/ps_motif_class.Rd
656bac58041b27c0fc011f9bc98d3d98 *man/ps_pvalue-PSMatrix-method.Rd
60a65e8ea874d9cbf323eb9db4ab7d7c *man/ps_pvalue.Rd
49e091d4e9a9318f3db24be80dac2afe *man/ps_results_table.Rd
5094661e8eb7f9d2f84c3d8a50583440 *man/ps_retrieve_bg.Rd
599846c3f85382b355f8b4f7510237ce *man/ps_retrieve_bg_from_file.Rd
eef57e2a8237d16d62f72ec00b86423e *man/ps_scan-PSMatrix-method.Rd
9ecc38fc6d6c406269cd6a266e499732 *man/ps_scan.Rd
a2ad47047e5ab70e0fdcae22f4cc4082 *man/ps_select_promoters.Rd
319279d78787e84eeee5100733357d53 *man/ps_selection_summary.Rd
9922f7e8e2a1df932a18b8f5c8837853 *man/ps_seq_names-PSMatrix-method.Rd
43f796c4273c0f6c70c09df8428239a3 *man/ps_seq_names.Rd
595d9fa062bbacfc56216d656e5795cc *man/ps_transcript_legend-PSMatrixList-method.Rd
b636bb55d74e9d29ba21bc79641120bc *man/ps_transcript_legend.Rd
9bcd3b1ad2e098cbfe239223374f73bf *man/ps_write_bg_to_file.Rd
2573784adc9d5b55551379452cf73690 *man/ps_z_table.Rd
d86278b28c093bb765d20c8afac6a2d2 *man/ps_zscore-PSMatrix-method.Rd
21a9772a323db819555d55ad824da78b *man/ps_zscore.Rd
2909c4ab80378381b5a9e63c6eab1207 *man/ps_zscore_heatmap.Rd
50eb2295632b4354b22706c8a79a5305 *man/pscan.Rd
1e13d12a023c4f70547bbae2b60929a7 *man/pscan_filtered.Rd
c41d43335c3540ac8cf391e48c2c4ade *man/pscan_full_bg.Rd
7ab26dbd8575d19be9267e3a459c0aef *man/show-PSMatrix-method.Rd
ebcb700dd8ce1c8f32a62b9c2ff057a3 *tests/testthat.R
fb1b64d476cbdbf5c60414e8de713b29 *tests/testthat/test-Argument_checks.R
cbf5d770a1c05df4b154d8bcd6473eb2 *tests/testthat/test-Background_backends.R
215848e915599346b14ba5afae123b76 *tests/testthat/test-Background_catalog.R
7aa13f51ff90b72181b13cfe36be7325 *tests/testthat/test-Build_Background.R
8c6676156706696116f223f153f72105 *tests/testthat/test-Full_background_legend.R
e7c0fa8bd5770d5f2aa8a2010d97ef28 *tests/testthat/test-Manual_contract.R
38ddcc94ff92c3a7f49fd6ea1f3bd393 *tests/testthat/test-Parallel_defaults.R
6657b859323dfa4585d6f24bca68f30f *tests/testthat/test-Promoter_selection.R
ce636978edf8d92745a623c9418a8732 *tests/testthat/test-Scan_and_post_processing.R
12a90fe71d2118194b36dc494a4c92ab *vignettes/PscanRQuickOverview.Rmd
f4ab76aaa416708c8d941310e10e6e53 *vignettes/PscanR_Arabidopsis_BPC.Rmd
0e6ed7bc2ebb00d8e9ab07cba6478952 *vignettes/PscanR_Custom_Background.Rmd
8eb7e8ecc47e4428b95174b92b55b743 *vignettes/PscanR_Mouse_HD_Retina.Rmd
122590d14db0fd7cd0ba4d15f59662c0 *vignettes/PscanR_concepts_and_input.Rmd
