6212b4fbb6837275ed4b27f6fb62466c *DESCRIPTION
873bee8ca7b65d221168c8b9959ef946 *NAMESPACE
9e6c19db30f52d36f2c50de20195d94f *NEWS.md
5ec75d81f0bab6ff4bd463a74f0a5ebf *R/add_frag_info.R
5b63d260d5fb838ebbc3751d5bca2773 *R/bam_to_bins.R
1aa4da4e56ca7457927b99273b4c05fb *R/bin_pmol.R
b0019297fab955c673ec815497c481fb *R/convertPairedGRtoGR.R
219f15b95766a2fda28c51ef0902263e *R/covg_to_df.R
d582eff9a536e97304ba6910cdc804d0 *R/data.R
d33af1b06360dc1ecc884f2f30c568a2 *R/find_spike_contigs.R
624a5750f76cb047ca3fa82711c0b4bb *R/generate_spike_fasta.R
d67a20ad5f314c77c7561642cf51a3c6 *R/generics.R
b20dc13b4c0bbfa64154f8d298cd8a81 *R/get_base_name.R
30c50600edf6e4ca1346ba9143862705 *R/get_binned_coverage.R
9505ad2dc3e4d4ce1fbadf193c47893c *R/get_merged_gr.R
de70f1b89200732ddebf696f353e8659 *R/get_spike_depth.R
f877ba42c1fd4e4ae20694f865708b55 *R/get_spiked_coverage.R
4ccecd78bb999f72c12a7574b71bb0dc *R/kmax.R
cca6eecb6603c66e7176802a1ab0549b *R/kmers.R
221d0cd1510dd8e567d28c91111953f5 *R/methylation_specificity.R
19f8029189c2682bbc7e295e496e1205 *R/model_bam_standards.R
22f4df9ad7319dabb3f6bba19704cbbf *R/model_glm_pmol.R
319405427049256885fdbd4f3ea0a50e *R/parse_spike_UMI.R
61641167b5692edc18cbc4a6605c5c46 *R/predict_pmol.R
9f8ecc86bcf48600b3570ee5234e334a *R/process_spikes.R
9222353cafd0cabdea9c0088e4717ee6 *R/read_bedpe.R
c9fcf6295229f07114fd85af336ce251 *R/rename_spike_seqlevels.R
3111065ad5fbd82461b6500970d11120 *R/rename_spikes.R
70a027e1770814980a5c0781f637fa12 *R/scan_genomic_bedpe.R
67e1538ddbb4d6199a5831c297237bd2 *R/scan_genomic_contigs.R
620e022d9159b2d9abb50048066fc7b0 *R/scan_methylation_specificity.R
5e6ae2b8dc49fd62f953d5b85c53a5da *R/scan_spike_bedpe.R
4b132127733d5be09bc6d8b22822f32e *R/scan_spike_contigs.R
4d1342e347246b4a3ae3fa7bd3f0c810 *R/scan_spike_counts.R
d75e0a18ec28c1398e515e158fd31b70 *R/scan_spiked_bam.R
3c9793f62ba70acbe1f20775c7440533 *R/seqinfo_from_header.R
ee9958877d2b7ecf220268a8caeacb56 *R/spike_bland_altman_plot.R
d3b66521cf91b5dab38a6d1f5c06dc34 *R/spike_counts.R
2a4ce18dbe55c9ed1cd0651794240538 *R/tile_bins.R
eb3cfde1e84fcdda7419568550e11536 *README.md
b19c35f08be1d9011f21ca8112a46b46 *build/vignette.rds
bc4339189a0984ecb76effb736dadcf4 *data/dedup.rda
03debe206c062af8d11c639aabbcbb18 *data/genbank_mito.rda
2e82b28c6f37f15f683b5871a980ea21 *data/genomic_res.rda
9c85bc6bb9cee8a4ceb91e326b0f8762 *data/phage.rda
482f83cf599de054d2b686fa89edbb9c *data/spike.rda
fb8fef4c0e781b652983e830d8f77186 *data/spike_cram_counts.rda
3d1d000fa0ebec2621787e51b98a0d6c *data/spike_read_counts.rda
39d18dd7a9dddb788248b1f1d6696d93 *data/spike_res.rda
8fc7d9a9fc9eba6927aee71368a43c84 *data/ssb_res.rda
9503a8ee2bd7c9f105845b448431ac71 *data/testGR.rda
b4a392c080f19797f49d7f7d45af8023 *inst/doc/spiky_vignette.R
82b8064d36e89b81a5c40ce55eff0822 *inst/doc/spiky_vignette.Rmd
ee9d274b7594bc12c85211d2bd90f3b2 *inst/doc/spiky_vignette.html
ffde27eb2a5544389ad1985a572f3251 *inst/extdata/2020_Human0.01_test.csv.gz
9a1f29ecdc563139a605aada01a2b208 *inst/extdata/2020_dedup_spikein_data.csv.gz
b626c518cdd15e56495273d1f12df120 *inst/extdata/GSM5067067_2020_6654_bedpe.bam
dfdc3312bd8a0aca47827dc4d2fdd698 *inst/extdata/cfMeDIPspikes.fa
0c229551fa1ddc50a8447bed481e3bea *inst/extdata/example.spike.bam
fe849fb50e870e4edd31007905acec64 *inst/extdata/example.spike.bam.bai
5713d518e749eb3d8aa2622a7e71120e *inst/extdata/example_chr21.bam
42567a81392213809236b88487f1ef6a *inst/extdata/example_chr21.bam.bai
3c7749b47e92e8164e43894498187b20 *inst/extdata/example_chr21_bedpe.bed.gz
a4b2d08aca35d1659cc5823cabe95df4 *inst/extdata/example_chr21_bedpe.bed.gz.tbi
83d823f024d15dcb8fc2b4fdaedb5bb7 *inst/extdata/example_spike_bedpe.bed.gz
db6b39c01ff4fb498183a2a814aa0552 *inst/extdata/example_spike_bedpe.bed.gz.tbi
1126d8dca655392fb5b574ac793fdfaf *inst/extdata/phages.fa
d239d6bfe1c3b17f2f3d0942b2348f1f *inst/extdata/spike_contigs.fa
dfdc3312bd8a0aca47827dc4d2fdd698 *inst/extdata/spikes.fa
9e11ee87e94d8ea54cad93e678f2e678 *inst/script/genbank_mito.R
27077582ef1819d569a2bdc3dceb16db *inst/script/loadDedup.R
c93ebcc29e106e95ad30166b4643ccc1 *inst/script/loadTest.R
e2034aa4cb737b7c624eeb3b64642af3 *inst/script/mergeBeds.R
ee7f21f02f5d97bb247a494dac6c62e7 *man/add_frag_info.Rd
a02a453a27c1d6b415c2b2d17d71f612 *man/bam_to_bins.Rd
dc35c7db26dc4efa9a55ddea601ef836 *man/bin_pmol.Rd
e416d1b60846bb9bfa61ad96988044d3 *man/convertPairedGRtoGR.Rd
dde5f203e78d2eb6e7ceb2c71be37cb7 *man/covg_to_df.Rd
ad82381ae1695c464a5d9bfb7f2c167a *man/dedup.Rd
d5687b64437671e8399429f2816d6068 *man/find_spike_contigs.Rd
1291bf88d39c9266ea828ad2337a97a3 *man/genbank_mito.Rd
f4076193e79fb93ac33c7cf101bf8805 *man/generate_spike_fasta.Rd
7196c43feb911faa2dcf67e295702ad9 *man/genomic_res.Rd
1c01479cdd98af8d2170639ffb4ffbff *man/get_base_name.Rd
c403e64b52fe8c2f1c009b7b4c6e1ef0 *man/get_binned_coverage.Rd
4bab17af76db38b696d0c6603f8b27f8 *man/get_merged_gr.Rd
2d481d40a923872ec878ccf96119ec6c *man/get_spike_depth.Rd
7da8ec5960e2eacb9e07c044fac21cb2 *man/get_spiked_coverage.Rd
74af385b5b5069b1b88569f7b5d4c853 *man/kmax.Rd
dba9f336a18611017dd2bad4a5a0f9ed *man/kmers.Rd
34ad535cea6ea7db9e94f9b59465cdc6 *man/methylation_specificity.Rd
812f8c3a70c8aa5e41ba624901b6761c *man/model_bam_standards.Rd
4647b0742e49f02112e429cc81033dca *man/model_glm_pmol.Rd
edbbe62897c9317bd7a0a2e0b7556ddc *man/parse_spike_UMI.Rd
95fa921d0e4f1d1b39eca9c88215755e *man/phage.Rd
a4fd2fdd906bd4d051bad8e4cd6d8cfc *man/predict_pmol.Rd
c384d53e180858884ca3bae76146119a *man/process_spikes.Rd
29cdbeca75d94e2d8ebb5e78e25220cd *man/read_bedpe.Rd
4075d16e086a63868050067e94d0130e *man/rename_spike_seqlevels.Rd
7f38ef5b555f9e356a71b7f3fbffbc94 *man/rename_spikes.Rd
1881097bd8b6a86f471cc87802318c9b *man/scan_genomic_bedpe.Rd
28169e35078d495b1cc4ce237b22a426 *man/scan_genomic_contigs.Rd
9fb0df4773c179f05952b149d51ce38c *man/scan_methylation_specificity.Rd
a67b86e7f304a9bc1f710f3c07d08213 *man/scan_spike_bedpe.Rd
ff0c28e81069f7cec79b012ce4ce2a7b *man/scan_spike_contigs.Rd
fcf17e64d502e0cf29380e7b72eec523 *man/scan_spike_counts.Rd
158040b3337784bf05fe9b833f660a3e *man/scan_spiked_bam.Rd
dbe83bcdc4776c2651c1825b20aa5e59 *man/seqinfo_from_header.Rd
cb702c7fc2ca0042f55bd055553419b9 *man/spike.Rd
f50b5b2e533bd13faace46f6503616a3 *man/spike_bland_altman_plot.Rd
323f4cb2a1d9cad88c4be689b2866e5b *man/spike_counts.Rd
3483e7591bac762d6454c317794f04f4 *man/spike_cram_counts.Rd
888f5c2c9cfb7a99f6458bdffc20b338 *man/spike_read_counts.Rd
1818a3a1b4220e70c1bd39d77b2a30db *man/spike_res.Rd
b407e76353fac08331f6dbceaaf8f651 *man/spiky-methods.Rd
716340547868c8205ecd362ac9922bf2 *man/ssb_res.Rd
246e05024e360edcb8887cf74a0bb8ca *man/testGR.Rd
73625041d4a66675fc660b04589c25c7 *man/tile_bins.Rd
a930792b44cb3f868e6d45bb25235ae3 *vignettes/nature.csl
7221dd92367bb3299409e990511fa0b0 *vignettes/references.bib
02fd293d638a96a534807cf405ffdacd *vignettes/spiky-small.png
82b8064d36e89b81a5c40ce55eff0822 *vignettes/spiky_vignette.Rmd
