4033ce9a1e8215cf99d6254e07d3c5b5 *DESCRIPTION
d10c0011944bc8182303bdad4e7c007a *INSTALL
6bac6312600acf9de3837855ff4dacf7 *LICENSE
29a9012941a6bcb26bf0fb4382c5dd75 *LICENSE.md
cbd08b5532e1c345bcf6ea1015fb6a3a *NAMESPACE
84a3aa44eaef214104a406533fa71a40 *NEWS
0eae151ea3ecfe51dc8ef0bde16fa76a *R/calculate_meth_site_transcript_cors.R
a80767273195a53249b99549ad9b131a *R/calculate_region_methylation_transcript_cors.R
fd8a4971b86c0dbe812c7511d2428647 *R/chunk_regions.R
3d4ff49499b19a9ee49eb44911238ac7 *R/genome_annotation.R
ab7ea064a7fa1b491f104e1b9d2a43f4 *R/granges_manipulation.R
e030cdeab937cdd0aadfb287e68bfc46 *R/kallisto_quantify.R
8926d3ab4a51a22d2bba42349a334dc3 *R/meth_rse_functions.R
e3bfc82de67e5855d0b98bf3c257a1f6 *R/methodical.R
8a0ba737d26242f90e7faf5788092f81 *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
16aed487c7d5674a9403e7d0f7fbdcc9 *build/vignette.rds
7b106b46149a348af6be553e055133f7 *data/TumourMethDatasets.rda
91218ac5471f28e6161ebf5a8aed3856 *data/datalist
d7f85ed1f014ec5f82e1d8d262d372d6 *data/hg38_cpg_islands.rda
ed6e70309f1e527c0fa6ea4df80b275b *data/hg38_cpgs_subset.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
6135e227d8d319913377c1c9aca5ddc4 *inst/doc/calculating_methylation_transcription_correlations.R
6bd365b359c796c3f91d6ce52f6b4bbd *inst/doc/calculating_methylation_transcription_correlations.Rmd
a172799123aef3c75ada645d8ae85f7f *inst/doc/calculating_methylation_transcription_correlations.html
81bc0a365e747fdf5e5c31484caa99e7 *inst/doc/working_with_meth_rses.R
075e6500e19828194bb59aa6a5680cf6 *inst/doc/working_with_meth_rses.Rmd
73577964b245c6ae2257a3b31776ab42 *inst/doc/working_with_meth_rses.html
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
a60f7662add6d473cda5abc62ad1630b *inst/scripts/TumourMethDatasets.R
ed6c3ea3b604d7bd63fc5853ad7b7154 *inst/scripts/infinium_450k_probe_granges.R
2f6c0d49ba0f4666264d63519516129b *man/TumourMethDatasets.Rd
09525c2542b3c9cb3f9753670a03abdc *man/annotateGRanges.Rd
eea491fcd4422c4c287d5a040168cc00 *man/annotatePlot.Rd
16083f1335780defd5a2455fe5e88379 *man/calculateMethSiteTranscriptCors.Rd
fbc6cf7ec27ffbdb3d2acac7fe75a33d *man/calculateRegionMethylationTranscriptCors.Rd
f3715f044f7348d08447343729ab2570 *man/calculateSmoothedMethodicalScores.Rd
c7c3f66fa700cf304a2238a74dcd35d8 *man/correct_correlation_pvalues.Rd
a297278acf4b20f950ca0214a68b0538 *man/createRandomRegions.Rd
4839ad7ec8aa2c3cb6f43ae2a67f15f1 *man/dot-calculate_regions_intersections.Rd
32ae0a101a9c0e172af978ba3395ba99 *man/dot-chunk_regions.Rd
a2335db2d46d6da9e0a1bc0537efa771 *man/dot-count_covered_bases.Rd
61103a407430f91675c47ae1a507d83c *man/dot-find_tmrs_single.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
0e4bff459c5649cb96deb84c4773a3f9 *man/expand_granges.Rd
6bd753468a3c4ddcc013b690d1dda23d *man/extractGRangesMethSiteValues.Rd
2ca02db9e5ecbc5b55ec91729c6cc9b5 *man/extractMethSitesFromGenome.Rd
1cc6fe48fd452a24cb95546f57574d87 *man/findTMRs.Rd
3a53ae2e16de10e09ee0bab7d9755471 *man/hg38_cpgs_subset.Rd
1e65fd047f00671a03966dab88f4d2f3 *man/kallistoIndex.Rd
8b06cf188f28ba18a8e89c478ec7825a *man/kallistoQuantify.Rd
a339364fa3f28545fc1f8cbbaee8d2c8 *man/liftoverMethRSE.Rd
a9f5bba9fa62f981390f6a62a4135fab *man/maskRangesInRSE.Rd
0f784e86aaca36bb2f65b7c9593b5a6f *man/methodical-package.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
de40157dd8ec454e483308002ace4248 *man/strandedDistance.Rd
936e40c23bed58c228349292fa4258a5 *man/sumTranscriptValuesForGenes.Rd
43a6fd8030bf61b08abd22d5da9eb4bb *man/summarizeRegionMethylation.Rd
1664ed1a85fedd1b0fc598af1c99afa4 *man/tubb6_correlation_plot.Rd
f626407808104c25e35257c639d6df2f *man/tubb6_cpg_meth_transcript_cors.Rd
d52f3452fb3eab61423e409bba540736 *man/tubb6_meth_rse.Rd
886d810fb600a267a72b5411737b4052 *man/tubb6_tmrs.Rd
57b3323de867f0f1c6f563885d948e68 *man/tubb6_transcript_counts.Rd
d346fdd901e16693302131b1dd2ba73a *man/tubb6_tss.Rd
e048f6199db30bee924745d59eef4066 *notes.txt
3eea21115047ba224f2d24569f8921fc *tubb6_example_objects.R
6bd365b359c796c3f91d6ce52f6b4bbd *vignettes/calculating_methylation_transcription_correlations.Rmd
075e6500e19828194bb59aa6a5680cf6 *vignettes/working_with_meth_rses.Rmd
