527676f677a028c526dc6d5dc1e5aaca *DESCRIPTION
547ba7370ac4609dc937e38690371aa7 *NAMESPACE
e670dea5bfad7dc44a90216e1b2b331f *R/FootprintCharter.r
201080478071ece4ecbba51a36262394 *R/FootprintCharter_footprint_detection.r
cdcd99e423d26e2e4bbee1268e945090 *R/FootprintCharter_plotting.r
64dc8b2193044b1dfe229cf2d3821f12 *R/FootprintCharter_rolling_mean.r
9755f26b78dc3a047b97ff8f900f8855 *R/composite_plotting.r
53d293872cf875777c96482216840532 *R/hierarchical_clustering.r
62e8d188a242a5d1f3bf79568c1153cc *R/methylation_calling.r
6a3788182520c72f766b7838dc2c87eb *R/methylation_calling_utils.r
5e8147ae942baa70fc31b8f3c8820d9c *R/plotting.r
3e10ea173f92f55d179370e04a0fb9db *R/sequencing_QCs.r
94efa8c0b0ba54c034dc3a5c96345ba1 *R/sequencing_QCs_utils.r
c9dd2c1ad8daa535aad50ef7e3982579 *R/single_molecule_sorting.r
f9fc970078801a3e5f5223d82515c4c8 *R/single_molecule_sorting_gw_wrappers.r
c6dc525db79fcdcc07bdfc786136bf1d *R/single_molecule_sorting_utils.r
266a68ab80b8cdb16037ac2a1a459eaa *README.md
7e84c292cc09d9d11ab3a152752a85c7 *build/vignette.rds
569192360dd903478ca29d376938ea8e *inst/CITATION
d2fc5b85c32301739fbb23e3a3c75025 *inst/doc/FootprintCharter.R
00addb1017134cc02d2fd2938917b6c6 *inst/doc/FootprintCharter.html
67bd565067c84552f5a76d3c232eec58 *inst/doc/FootprintCharter.rmd
66790292ba12fae4dbd0100fb3ef567a *inst/doc/methylation_calling_and_QCs.R
751454fe76be26030f2ba2b7f8096da5 *inst/doc/methylation_calling_and_QCs.html
a2c60a5966f8bd6ac9618f34d7116cd9 *inst/doc/methylation_calling_and_QCs.rmd
44d6f337aa7080b0bfd4194950a606b8 *inst/doc/single_molecule_sorting_by_TF.R
1602e9391ffcb059aba56b2f75c7cc16 *inst/doc/single_molecule_sorting_by_TF.html
4b51603de94359f253f736c95a6ec02a *inst/doc/single_molecule_sorting_by_TF.rmd
5495146803fcdfc4fe5386764d96c26a *inst/extdata/KLF4_chr19.qs
7b2cc680ae725b7fcdcd5e6f03b21b50 *inst/extdata/MethRateCorr_AllCs.png
7913fee5255f5d4e9676377df21336ff *inst/extdata/MethRateCorr_GCHs.png
9ae047198f1607b2c62cdf7ecd858b6d *inst/extdata/MethRateCorr_HCGs.png
c00c780bdab2044880d7302c75629f06 *inst/extdata/Methylation_1.qs
7bea911abd6a2abae7d6f6c25a1c5a32 *inst/extdata/Methylation_2.qs
3a73dbfa13f6210c1ca9e377704a2a64 *inst/extdata/Methylation_3.qs
f33ed7b066e1952ec828189e20ad6a9c *inst/extdata/Methylation_4.qs
9b0d9c116499dea7dae4f441d1371e6b *inst/extdata/SNPs_1.qs
08afbbbd3f6afa39995b1f0284c1fe85 *inst/extdata/SNPs_2.qs
1a8bd759b48b8d7ee43b35107bb59d59 *inst/extdata/TFBSs_1.qs
884144ade131ff3cb834086bef84829d *inst/extdata/TFBSs_2.qs
87865feef76a29ffffef1e1d7c72bfad *inst/extdata/TFBSs_3.qs
7a9dab12e219e3885d1c859aef6261ee *inst/extdata/TFBSs_4.qs
bb117a1e7c0fa18badf56ef51303252f *inst/extdata/Top_bound_REST.qs
0df2df91ec16496213e388a4d02cd6a7 *inst/extdata/cytosines_to_mask.qs
79c82996f73eaf63ffc7b23b36d2f8e2 *inst/extdata/gw_sorting.qs
151b52665cd18689c8eca8cef50740ab *inst/extdata/low_coverage_methylation_correlation.qs
aa0a766a7de6ca9ed748c5e2af84ea19 *inst/extdata/rest_composite.png
4a08106fa280d7853202778b4b929729 *man/AggregateFootprints.Rd
3e01c0b4f29830bb3a79a05e4e38d628 *man/AnnotateFootprints.Rd
2a0dc8b3234e32a4bf6b58dd780fba66 *man/Arrange_TFBSs_clusters.Rd
e06921595db86ff6584f1927bd1dc9e9 *man/BaitCapture.Rd
824bc2b0db057befc944408d842dd1cb *man/BinMethylation.Rd
1d75137505e3ff194596540aad2a3c99 *man/CallContextMethylation.Rd
0235f0fc82c2a20b59bfd3c200d116fa *man/CollapseStrands.Rd
db98df79589a92c531328583d48c1a3e *man/CollapseStrandsSM.Rd
1552832385d61e479279d65cd1dba785 *man/CollectCompositeData.Rd
a50d6e058363bd470921b83607613e3e *man/CompositeMethylationCorrelation.Rd
7e7ee380e4a5bc1d96ff9207b79b8519 *man/CompositePlot.Rd
ca01403e6c4631e1a20c4d9efa35bb70 *man/ConversionRate.Rd
409059b19a70fee1a838bc8fe475511d *man/CoverageFilter.Rd
58f213006c6d291dd0a32968a6b28876 *man/Create_MethylationCallingWindows.Rd
8ed8fe6deb31e4dd2af3db180965826e *man/DetectExperimentType.Rd
d8370f9590898a8581d97a184d76c967 *man/DetectFootprints.Rd
98add841e5c455a57cee745256158392 *man/FilterByConversionRate.Rd
059072c5124c10f1ae5473b5d8568ab2 *man/FilterContextCytosines.Rd
ab2255b15a23b340f15bc1cb3495a409 *man/FootprintCharter.Rd
d46f88a5fbfdc2c59787cacad0307feb *man/GRanges_to_DF.Rd
80235ccdd2fae8a0c3df039692a8998b *man/GetQuasRprj.Rd
34d6b5870f2d9878ae166262317124f4 *man/GetSingleMolMethMat.Rd
ef4b878bb48eef2bbff942ca90026f35 *man/HierarchicalClustering.Rd
e366ecee6a2b4a41645975196075b7ad *man/LowCoverageMethRate_RMSE.Rd
ca9a42d6c7a0c0207c229d5646f57064 *man/MaskSNPs.Rd
13599afd206f98c944e2bcf1ce41898a *man/MethSM.to.MethGR.Rd
a27cbe6e56b03b91f36ef664d0f22e43 *man/MethSM.to.dense.Rd
bd5122e49f6c5ef30cbaf7c2f49f5de0 *man/PlotAvgSMF.Rd
45d87bcc2b97f192a9e5829e2ed4b4e0 *man/PlotFootprints.Rd
1c53b90113b8e77daea07c3c9ab81f57 *man/PlotSM.Rd
a9e50f1fbc013013430f82cf9ae7b91d *man/PlotSingleMoleculeStack.Rd
4c171aca9002890ef09dccfee614ced6 *man/PlotSingleSiteSMF.Rd
5bed2775bb2699c64488507965f8b8c8 *man/Plot_FootprintCharter_SM.Rd
edfbea11e6db51cb9075dfcdf276dddc *man/Plot_LowCoverageMethRate.Rd
6ee77da3dcf21c391d196a8935e4f690 *man/Plot_LowCoverageMethRate_RMSE.Rd
f39184024d0048f8647288bb1c231fda *man/RollingMean.Rd
5f817f0e00659c6a01fee1666a487286 *man/SingleTFStateQuantificationPlot.Rd
5cfdf04f796a6d35dad15f04a38fdfad *man/SingleTFStates.Rd
ddcb8fd7a48b38f30687f5d92f92aef8 *man/SortReads.Rd
9962b3fc9ae0d0d4d9b0a564e2714e69 *man/SortReadsBySingleTF.Rd
f3a8f51ce355d283d7e51e1eeb275c37 *man/SortReadsBySingleTF_MultiSiteWrapper.Rd
953c6e50f1151dc2dce0e11e2cb50f7f *man/SortReadsByTFCluster.Rd
985ba2c6c25b3f2e75ed130f2bf9ba11 *man/SortReadsByTFCluster_MultiSiteWrapper.Rd
b2b24ffa9709776f312004d8747cbe97 *man/StateQuantification.Rd
de4645aab3386b809a85bcef4fdafbab *man/StateQuantificationBySingleTF.Rd
52318ad2fe770b0d8bf7bd4927894fde *man/StateQuantificationByTFPair.Rd
35189b7fad4be75b7a2ccddadb1b0a29 *man/StateQuantificationPlot.Rd
082c35fbb3c8b6616488a6db252bf31f *man/SubsetGRangesForSamples.Rd
a82f99fb7a271a67e5d80910da84d964 *man/TFPairStateQuantificationPlot.Rd
122f2b7372481e3e20f78b69de3447d0 *man/TFPairStates.Rd
a4bb6b35bfed1e034a354c5a325b314d *man/cbind_fill_sparseMatrix.Rd
a19958ebc29724514564e23c9e154a2c *man/colMeans_drop0.Rd
814fbd84c023b40af6b159fd51245f29 *man/dot-detect.footprints.Rd
de545887951277de64bb7228f3a032b9 *man/fill.empty.columns.Rd
514dfc82b1467ad4ede9588d533ffe9f *man/filter.dense.matrix.Rd
874300b32b00b7f073858c505634c239 *man/filter_reads_from_MethGR.Rd
fb927fa3451775aee6ad100b2188ba05 *man/full.join.granges.Rd
e002d9e4c66a4ab7b79b99578eb3ddc8 *man/matrix.sliding.window.average.Rd
9c00f5746fe7c280d183cf04c3b0d7e0 *man/panel.cor.Rd
4fa37feeac4986c1de8ea429cf2b3739 *man/panel.hist.Rd
caea95b14b3002f00fee1e7226c5d717 *man/panel.jet.Rd
5b39ec07002aa69f712dc0e3d64b46c2 *man/rbind_fill_sparseMatrix.Rd
21d48e2eabe42d5bed02e01eb640c293 *man/rowMeans_drop0.Rd
6801b32c8dc629a75c2b52769a596f60 *tests/testthat.R
4f1de9419761ad7f1a118227de9b4ed1 *tests/testthat/test_methylation_calling.r
4b3fb607efb913cfcf536621bfe18c2e *tests/testthat/test_sequencing_QCs.r
7db02cfa8761a5cd49565ed58a2ba16a *tests/testthat/test_single_molecule_manipulation_functions.R
67bd565067c84552f5a76d3c232eec58 *vignettes/FootprintCharter.rmd
a2c60a5966f8bd6ac9618f34d7116cd9 *vignettes/methylation_calling_and_QCs.rmd
4b51603de94359f253f736c95a6ec02a *vignettes/single_molecule_sorting_by_TF.rmd
