b95dbb0dfa57e70536eb6b2c5ff1e9fe *DESCRIPTION
d10c0011944bc8182303bdad4e7c007a *INSTALL
6bac6312600acf9de3837855ff4dacf7 *LICENSE
29a9012941a6bcb26bf0fb4382c5dd75 *LICENSE.md
fdeb2666c1b91a72f929762dbe97b7fa *NAMESPACE
84a3aa44eaef214104a406533fa71a40 *NEWS
0eae151ea3ecfe51dc8ef0bde16fa76a *R/calculate_meth_site_transcript_cors.R
02c445c440640a784760d6e8f4f72fe5 *R/calculate_region_methylation_transcript_cors.R
fd8a4971b86c0dbe812c7511d2428647 *R/chunk_regions.R
a0a74760417a11e4e300a9ba9a0b9b50 *R/granges_accessory_functions.R
c4cf37968143e2d7e080420755497ef9 *R/make_meth_rse.R
ec40995498d716ceb27eac1e5f8c09c3 *R/make_meth_rse_accessory_functions.R
9d056ba5d6d5d0b065c9ca2cd5b7aa7a *R/meth_rse_functions.R
e3bfc82de67e5855d0b98bf3c257a1f6 *R/methodical.R
355d7388ac9392556754ac158f55e03a *R/object_documentation.R
e3536f436b85c756e9b9aed291877cb2 *R/plotting_functions.R
4353b2fc4550fcceb165916c25b858b5 *R/rapid_cor_test.R
889c3cb4f7daa3a57d1603ec69b1b835 *R/summarize_region_methylation.R
73c28a98dcd05189469fb700e48bf264 *R/sysdata.rda
22cff4804f1fd090e9fbca7a483bd5f9 *R/tmr_functions.R
45a6c7d90bc32dc1a865d82d0e152e32 *build/vignette.rds
929500e1fddfb0c82efa0a61b4903d5c *data-raw/example_objects.R
5817f771c8ee8602c0c63e25aa061ea8 *data-raw/infinium_450k_probe_granges.R
37de7c9c29f754168b2e20675b1c6cbc *data-raw/subset_cpgea_bismark_files.sh
3af8f6667f60eada02bf7f2989c58d24 *data/chr11_subset_hg38_cpgs.rda
c1708bfd4437ff812a28f9eaccbea4f3 *data/chr1_subset_hg38.rda
abf06c6f1343d382f6d9aa50445e5c06 *data/chr4_subset_a_thal.rda
44003db94f1b99555dca1c4d5e36ef8e *data/datalist
c18a25cd1eb2e7054912d606a9591183 *data/hg19_chr18_cpgs.rda
d7f85ed1f014ec5f82e1d8d262d372d6 *data/hg38_cpg_islands.rda
4a4c04848d60c9602821ca3960e738fe *data/infinium_450k_probe_granges_hg19.rda
e6335fb5e862dec1ee185aad20372cff *data/tubb6_correlation_plot.rda
ae7167a572ed3c92fce674a8b3b36e93 *data/tubb6_cpg_meth_transcript_cors.rda
c121a4497cc12b5f9c422b4c5d66c729 *data/tubb6_meth_rse.rda
6a3420ac7a4699bcdd485f705626bc33 *data/tubb6_tmrs.rda
da384530a192f926933ae8643373c9a0 *data/tubb6_transcript_counts.rda
dd90ed10b825e27c903bbcd7d12d12e0 *data/tubb6_tss.rda
6bbf9dfadfbc4e74f1e3d4379f2e8adf *inst/doc/calculating_methylation_transcription_correlations.R
13aa7f50b27f62ee676b628f1d27269d *inst/doc/calculating_methylation_transcription_correlations.Rmd
0e26bf670750d02f3e380f5a6f49a215 *inst/doc/calculating_methylation_transcription_correlations.html
c15169e05c2cddc55e0db8a0861959dc *inst/doc/working_with_meth_rses.R
f35a5806a7d2ed7886514994b75dc60c *inst/doc/working_with_meth_rses.Rmd
060ed7401b7acfdd23456af6e0d73e9a *inst/doc/working_with_meth_rses.html
4b1d1b3eda4b668777cfa1ad1e09c0b7 *inst/extdata/N100_WGBS_mC_Identification_GSTP1.CX_report.txt.gz
5f1b64b1550f67cfec3efb514a775dce *inst/extdata/N103_WGBS_mC_Identification_GSTP1.CX_report.txt.gz
c793a64ef52405945933fb04fca45dc0 *inst/extdata/T100_WGBS_mC_Identification_GSTP1.CX_report.txt.gz
b5aa44c8ad84e5eb323c8dd2108ed354 *inst/extdata/T103_WGBS_mC_Identification_GSTP1.CX_report.txt.gz
a6519cf6514c846d5bdec70fbb3ba0ca *inst/extdata/TCGA_05_4384_01.txt.gz
2a39e2eca31e7e35f5a35ce8535bb8b2 *inst/extdata/TCGA_05_4390_01.txt.gz
3817bb3564531997b43fa6fbc9025034 *inst/extdata/TCGA_BRCA_A0CE.bg.gz
67bf42bfdb3742661c9de4cfeaf7cfd1 *inst/extdata/TCGA_BRCA_NA0CE.bg.gz
447a3de2aaf4fca8db738f400f714849 *inst/extdata/TCGA_COAD_3518.bg.gz
0fc41751d4e7f9fa45ab9f582bd745a5 *inst/extdata/TCGA_COAD_N3518.bg.gz
d16d98f34c87ab3920fb270e478c4d32 *inst/extdata/tubb6_meth_rse/assays.h5
bfe5838ffa12a638db0ec6ae93067a3f *inst/extdata/tubb6_meth_rse/se.rds
eea491fcd4422c4c287d5a040168cc00 *man/annotatePlot.Rd
16083f1335780defd5a2455fe5e88379 *man/calculateMethSiteTranscriptCors.Rd
fbc6cf7ec27ffbdb3d2acac7fe75a33d *man/calculateRegionMethylationTranscriptCors.Rd
f3715f044f7348d08447343729ab2570 *man/calculateSmoothedMethodicalScores.Rd
62f8130fbfcd89b6a972ea27b44d4243 *man/chr11_subset_hg38_cpgs.Rd
776c21b157f4ae3960332ca8128a16a6 *man/chr1_subset_hg38.Rd
f0dcfe384145cd24d05490d7487b2a10 *man/chr4_subset_a_thal.Rd
4cb5c9abcef0084ca3e1a2651a273a4c *man/convert_rse_to_bsseq.Rd
c7c3f66fa700cf304a2238a74dcd35d8 *man/correct_correlation_pvalues.Rd
716aaf8071cda48f891661fe4d11dc4d *man/dot-check_input_files.Rd
32ae0a101a9c0e172af978ba3395ba99 *man/dot-chunk_regions.Rd
417a8951f1fe07dcc1a077fc2c920659 *man/dot-collapse_strands.Rd
c2406cc41fc8d2b3922d90be71c64ca0 *man/dot-create_meth_rse_from_hdf5.Rd
61103a407430f91675c47ae1a507d83c *man/dot-find_tmrs_single.Rd
4e7203e84f3fe250b149629c535381d3 *man/dot-make_meth_rse_setup.Rd
6c9d633677925b9a774193b3c1432d28 *man/dot-set_meth_df_columns.Rd
a1c1a5320243320982115b8b54a66180 *man/dot-split_meth_file.Rd
ddc5f619a5d14de38c4114df0cbc8f7d *man/dot-split_meth_files_into_chunks.Rd
f90f96fca2ff6bf59502fe4063ea15b7 *man/dot-summarize_chunk_methylation.Rd
5bd4012e42cc88a3df365baa3fc49974 *man/dot-test_tmrs.Rd
b17fe7a3568282b9d03226c93b73d53e *man/dot-tss_correlations.Rd
dd7571b5ace015c74d565f77dd642c89 *man/dot-tss_iterator.Rd
422922c26694e896d7151b5c53e6cbb1 *man/dot-write_chunks_to_hdf5.Rd
fb4af05d69330315210f8f13c77aca47 *man/expand_granges.Rd
fc04e685ebdf6c927f9f5dfa8bb01b62 *man/export_bedGraph_from_rse.Rd
6bd753468a3c4ddcc013b690d1dda23d *man/extractGRangesMethSiteValues.Rd
537149c07796b5ff3260aa6f3441f79c *man/extractMethSitesFromGenome.Rd
1cc6fe48fd452a24cb95546f57574d87 *man/findTMRs.Rd
a7749c79fa46d39cb654f6382c07a266 *man/hg19_chr18_cpgs.Rd
2446c0794fcc70963246b43353321101 *man/hg38_cpg_islands.Rd
113e2e67fb9f957af85407fcea23deff *man/infinium_450k_probe_granges_hg19.Rd
ff2baa67959a65b3697f4b1f429eefa1 *man/liftoverMethRSE.Rd
1c2ff11931bb11d2a0f37df0db59cebb *man/makeMethRSEFromInputFiles.Rd
a9f5bba9fa62f981390f6a62a4135fab *man/maskRangesInRSE.Rd
0f784e86aaca36bb2f65b7c9593b5a6f *man/methodical-package.Rd
5db81021ed5a648a4ae11163a9f9f282 *man/methrixToRSE.Rd
5d894713c93c6450f62d70a0eba608b2 *man/plotMethSiteCorCoefs.Rd
165995af0205ca3eb8fb5b663579fdab *man/plotMethodicalScores.Rd
c6a02067455f27410f31d7c8a30d179b *man/plotRegionValues.Rd
01f471f3f691100ac49740054f2697ae *man/plotTMRs.Rd
b56c3edabbefc29902e5e666db90653e *man/rangesRelativeToTSS.Rd
b8e489cc7b81bf04ab211d405b5b42fb *man/rapidCorTest.Rd
84f684704b6e8d74a3e39f8ff37bf795 *man/sampleMethSites.Rd
1b7d3f088ecf1942a5e9e63749ddcc04 *man/strandedDistance.Rd
43a6fd8030bf61b08abd22d5da9eb4bb *man/summarizeRegionMethylation.Rd
1664ed1a85fedd1b0fc598af1c99afa4 *man/tubb6_correlation_plot.Rd
f626407808104c25e35257c639d6df2f *man/tubb6_cpg_meth_transcript_cors.Rd
aba1bd6cb5f5dfaabe321fd4d0e59378 *man/tubb6_meth_rse.Rd
886d810fb600a267a72b5411737b4052 *man/tubb6_tmrs.Rd
57b3323de867f0f1c6f563885d948e68 *man/tubb6_transcript_counts.Rd
d346fdd901e16693302131b1dd2ba73a *man/tubb6_tss.Rd
328701deb7bb43e5ee3f4d574f68543a *notes.txt
13aa7f50b27f62ee676b628f1d27269d *vignettes/calculating_methylation_transcription_correlations.Rmd
f35a5806a7d2ed7886514994b75dc60c *vignettes/working_with_meth_rses.Rmd
