c2ab17722300d8ff3821a30d5198d97e *DESCRIPTION
0cc7b62d06a3884a88bf5ff7bb92fe9a *NAMESPACE
5571b12047057dd8c57c7fe71055803a *NEWS.md
1dbca0ff8e657d1e6d5fbae582b45c2f *R/ComBat_NoFiles.R
c28d378a38260c6ff528617aed6cf4b1 *R/CpGClustering.R
8f488611a4845fd20f71873a6b09b5f3 *R/EpiMix.R
a5b67a57cc8232747295955b0ad443c2 *R/EpiMix_helper.R
36ed244a7b56226f0f36aa4c4890b6ab *R/GEO_Download_Preprocess.R
a19fc020102fad3e35ac7de38878dcb4 *R/GetNearbyGenes.R
a31134e575cafc6aadfd6e6ddf7f03b6 *R/MethylMix.R
133a84272f0a988a1f01e487fd8e0a46 *R/PlotGene.R
d93c0c1af641ea36952c147fda7d01bb *R/PlotProbe.R
1aba0a678c18f45cfd377e054fd8220a *R/Survival.R
922b228e92fd35771c5a7b4eeff1ad1f *R/TCGA_Download_Preprocess.R
c96c32b0a626ea6fa8bbd1113b126325 *R/TCGA_single_command.R
7b72dee7329cf161d454b39c56f2228c *R/correlate_gene_expression.R
c921fd8de507c5247623d3a09d4ceb5d *R/miRNANetwork.R
79756ae067f1b706b9a5be33598f516e *R/util.R
29074a923333d9a81b7c9e05272c6422 *README.md
cddfd664d897da86d45bfbdeffb4353c *build/vignette.rds
88fe1f7c73ba0099d513959a9574749e *inst/doc/Methylation_Modeling.R
1cbd810b2e3f5853ea5b5ef0974956f0 *inst/doc/Methylation_Modeling.Rmd
a30be773d415b513d434191509401d04 *inst/doc/Methylation_Modeling.html
0d2f2d5f7946ad6b6198e0e6f94eedbf *inst/unitTests/test_enhancer_mode.R
96d8be4f8dea071ea86e69e039964c95 *inst/unitTests/test_lncRNA_mode.R
5bad22fa57292d92dc94afd3a778f9ee *inst/unitTests/test_miRNA_mode.R
98d0f53f5397038b6b8550cced6c5288 *inst/unitTests/test_regular_mode.R
98ea806755a462c25ac767c7cd731484 *longtests/test_GEO_download.R
6052a097b894cc29984e0c6ce09254d3 *longtests/test_TCGA_getData.R
5d6463b7614f7c0a132ea1b521ba2c1a *man/BatchCorrection_Combat.Rd
927a9c75d6cfa574225d779c29480132 *man/BatchCorrection_Seurat.Rd
1ab8a57e0304bd2222de639c585cc78d *man/ClusterProbes.Rd
39eb4842c18e13a518bc4695326214bb *man/ComBat_NoFiles.Rd
af39f557716dd3ba203e340f6dd36041 *man/CorrectBatchEffect.Rd
189d67bdc42c219aba33feb736985f63 *man/EpiMix.Rd
0195fd75bddec3077fb6e7fead17c124 *man/EpiMix_PlotGene.Rd
6d3630a44e0a1238f2582e47573a63ec *man/EpiMix_PlotModel.Rd
f56307168b4f1ab2eac0f51c507a66e4 *man/EpiMix_PlotProbe.Rd
f896da0a5adb0c92e7622d367365490f *man/EpiMix_PlotSurvival.Rd
caa54afd64ccfb5532e516577e9a9dc1 *man/EpiMix_getInfiniumAnnotation.Rd
f4cc8cefa2468ab0aa33623eeabe0bb6 *man/GEO_Download_DNAMethylation.Rd
16b06b4640257cfa5d9ed21c236824fa *man/GEO_Download_GeneExpression.Rd
7dc02539831da988f7021b3fae57a682 *man/GEO_EstimateMissingValues_Methylation.Rd
0491d180b32881127f8e3eaa2f2c4785 *man/GEO_EstimateMissingValues_Molecular.Rd
7aa96941f69551e937390630006cbf8a *man/GEO_GetSampleInfo.Rd
fe1b6bec52ce76db032aabd1c2c79538 *man/GEO_getSampleMap.Rd
7c3fcbef72376a690e88a570a8d192f7 *man/Get.Pvalue.p.Rd
379aaa3bea8a7c14abf3c6204ab0cfc1 *man/GetNearGenes.Rd
a4c56daa96de8704c59be7317a5e2ac6 *man/GetSurvivalProbe.Rd
bf403897bf745751e2e1ba7b36cd2ddd *man/MethylMix_MixtureModel.Rd
d1ae59a8199333b01c73f402cee0e5f4 *man/MethylMix_ModelSingleGene.Rd
deae580fdcb7169a063b3bae74b4058c *man/MethylMix_Predict.Rd
b1cab898d8be6f502a918695d271e5d6 *man/MethylMix_RemoveFlipOver.Rd
c41df4a3b0cb041170961afb8e7229bb *man/Preprocess_CancerSite_Methylation27k.Rd
b0d44c31ed58a2c391d9d380ab4df08d *man/Preprocess_DNAMethylation.Rd
588dd2638159d200c4699936f88be529 *man/Preprocess_GeneExpression.Rd
8451f1bbd905c9ce747cc790cd0e19f3 *man/Preprocess_MAdata_Cancer.Rd
7f8e15c840bd0a51b9c43a34916f2a86 *man/Preprocess_MAdata_Normal.Rd
9e6dcdad1b44bc4e656b9db79dbb28e8 *man/TCGA_Download_DNAmethylation.Rd
0f284e6b3247d0da5395eb3a1175c492 *man/TCGA_Download_GeneExpression.Rd
e59ba4753ac905ec41122566192017a2 *man/TCGA_EstimateMissingValues_MolecularData.Rd
1aa94f02bef332ed30a071558973ec1c *man/TCGA_GENERIC_CheckBatchEffect.Rd
42eece64f0593da4146e82f4841953cc *man/TCGA_GENERIC_CleanUpSampleNames.Rd
f0acbf59f012c90c3600beea1e16e980 *man/TCGA_GENERIC_GetSampleGroups.Rd
5be5156dfebd4c7fb43738662de3c1ee *man/TCGA_GENERIC_LoadIlluminaMethylationData.Rd
5a8ca7cda2365de1f2ce54fa80c4d841 *man/TCGA_GENERIC_MET_ClusterProbes_Helper_ClusterGenes_with_hclust.Rd
6c8ce443e2c599c8bd0c0a50ef86d8c2 *man/TCGA_GENERIC_MergeData.Rd
985a0b617f8d0eebb7cdc69b5c61d920 *man/TCGA_GetData.Rd
a20191658e15d85a62dc21340d08cdaf *man/TCGA_GetSampleInfo.Rd
46aa913a21340c49242183fa39d27d95 *man/TCGA_Load_MethylationData.Rd
9e35ebf05fd5a134cc571eb2bb9bfbae *man/TCGA_Load_MolecularData.Rd
39a6a00049ab012ba68b41bf26a8867d *man/TCGA_Preprocess_DNAmethylation.Rd
615e3bbe167225d101c6dcda29529fe6 *man/TCGA_Preprocess_GeneExpression.Rd
a5589c531df7837517affa10848305b8 *man/TCGA_Process_EstimateMissingValues.Rd
b92f0f8112f973923457f91aa4325201 *man/TCGA_Select_Dataset.Rd
53b19c44519f8d67196dc5b3d1739f42 *man/addDistNearestTSS.Rd
2ff7796859cc8196c16dc610c83860a3 *man/addGeneNames.Rd
54f1283505459a9ae693dc15b09e2510 *man/betaEst_2.Rd
422c83e53688bf5c77ee3e2fb4002a68 *man/blc_2.Rd
c20f4726687aa342e4460ae368ddd413 *man/calcDistNearestTSS.Rd
86186a2fe886695eaa940daeac574eca *man/combineForEachOutput.Rd
6fbf3390640f1fd49627a556827797fa *man/convertAnnotToDF.Rd
00a3dba3057465646d5f41fa25b9affd *man/convertGeneNames.Rd
b9f4da965041d380efa47b843866160e *man/dot-extractPriMiRNA.Rd
f28ca9ba4c5db3d6389b1b4f21046ade *man/dot-getComp.Rd
ad10a827b69d7db9424ef78d221b03e7 *man/dot-getMetGroup.Rd
e6a6eb08c4bcf2b6032580dcf15371ff *man/dot-mapProbeGene.Rd
7b164828579d708f57088e808b88eccc *man/dot-splitMetData.Rd
842b90f53343a5215f55cee5f17d35ee *man/filterLinearProbes.Rd
cc2f303905b947960f53277ec6b0be38 *man/filterMethMatrix.Rd
09d7079b29072d4adc522a6937985fdd *man/filterProbes.Rd
ecfa12f43c2910c31d460334991c6fe0 *man/find_miRNA_targets.Rd
b1c0ece81fc411198b9b52bd21ca2778 *man/functionEnrich.Rd
08f60c976a696957026655f1ef592291 *man/generateFunctionalPairs.Rd
1f3e644194a52552f938b60e39f3c1f3 *man/get.chromosome.Rd
77a49d487c6cea7483f161f6668e67a1 *man/get.prevalence.Rd
d947ef59940d28403b761ce11f4006d8 *man/getFeatureProbe.Rd
812e32eea9864b5ade3575788b730112 *man/getFunctionalGenes.Rd
28d6ab21c534c319c3eed2b3778e3988 *man/getLncRNAData.Rd
51f63d4ebffa2717546ac2c22702f1e0 *man/getMethStates.Rd
682c79bfd73172e5aa68728d4e54ab95 *man/getMethStates_Helper.Rd
e92c8bad78f35d5ecc2e877852b90165 *man/getProbeAnnotation.Rd
9ce572abb8c269525aac8ea9640cdb26 *man/getRandomGenes.Rd
500435284976b30b272924f8c7681f92 *man/getRegionNearGenes.Rd
57c477a2ee373df1f3e70a8f905fe8d6 *man/getRoadMapEnhancerProbes.Rd
07ebe78254d9641f5ff7f214a1e95fed *man/getTSS.Rd
76e601a2ed2d33cf30806cb6a597fc57 *man/get_firehoseData.Rd
87e74aa6db2447e9e4fa5e5e008c0381 *man/mapTranscriptToGene.Rd
c19839b3236b9fc27753e52672292554 *man/predictOneGene.Rd
058d74a223e5bf1091238c875f40d1b2 *man/removeDuplicatedGenes.Rd
ba6e57743f9436311484ed3b805b7ea2 *man/splitmatrix.Rd
3783bdc320167aa4deaefe80498bf216 *man/test_gene_expr.Rd
a0e1e591135e9adf622dbeb11fc4c9b0 *man/translateMethylMixResults.Rd
788e949c53ddf7d1fed914ad368009a5 *man/validEpigenomes.Rd
2b59d720eaa821bd8d17402b228cf17a *tests/runTests.R
1cbd810b2e3f5853ea5b5ef0974956f0 *vignettes/Methylation_Modeling.Rmd
ce6f13a62168b08f29055a2cee8d9939 *vignettes/figures/Workflow.png
7201068177d1cded17073f4fd006a46c *vignettes/figures/plot_gene.png
7581500487b9ddb4ad8701a0337be2b9 *vignettes/figures/plot_probe.png
982e7cabb96c950da81f1e2fc81ad9c8 *vignettes/style.css
