0b1d4cd5969d4d80e91b3e9326f6c086 *DESCRIPTION
86d3f3a95c324c9479bd8986968f4327 *LICENSE
c4b240ff7af9ce384f1d545d43dece9e *NAMESPACE
838cf7a420209c4380cc79c4eac5291a *NEWS
e901bf56efeab09a3b31522a74f06853 *R/amaretto_download.R
6121274dd42099f18829b93ac08203da *R/amaretto_functions.R
c49d334a5efb2fa3b56e288af394d54d *R/amaretto_htmlreport.R
3143bcc42e44a5db76703a9901094006 *R/amaretto_initialize.R
b571bb1307ba7165628e65bf2fda2a75 *R/amaretto_preprocess.R
ffba55ec5b4cac9547a495b6965770ed *R/amaretto_run.R
10153dc74979622530e55ee9a020edba *R/amaretto_vizualize.R
1b01e843b4f26f1fd01f820d7f148660 *R/data.R
b84cb30077a82c4cb961584464f42041 *README.md
1146a86032c1440c1058193c4bee1f20 *build/vignette.rds
90eb3ce8affdbeb0b2919b7d65938e8b *data/BatchData.rda
bd1b89e8e422feb18ff2e40e2f3f6598 *data/Driver_Genes.rdata
a951941ea200487862e68500bcee1695 *data/MsigdbMapping.rda
5f44d61f2af8aee23521d73eef210a95 *data/ProcessedDataLIHC.rda
1c521b4566fc8f41a012419cce94ec22 *inst/doc/amaretto.R
8e09f1205bf130ee9474c4bc8ca658e4 *inst/doc/amaretto.Rmd
d6ccfbca8ade370cb813cb24656dd3ae *inst/doc/amaretto.html
10243cbf314d478615231cb9e26e2ade *inst/extdata/Module1_LIHC.png
fdfb5257ae030d70fa050a06995c80bb *inst/extdata/logo.jpg
59132bd6a76ff7868eb357d90f18e360 *inst/templates/H.C2CP.genesets.gmt
1672a63a8bca58f3cf43ed992817e532 *inst/templates/TemplateIndexPage.Rmd
49a558f7763c35bcd7c8bd2db09377aa *inst/templates/TemplateReportModule.Rmd
a8a33835795ac68ada41ab9bd72810c0 *man/AMARETTO_CreateModuleData.Rd
12b4539f940ffec3010602422b470f75 *man/AMARETTO_CreateRegulatorPrograms.Rd
f6716991bf2af132c839954fdff7d2a8 *man/AMARETTO_Download.Rd
562397504de2abb434a97af0ee0ef018 *man/AMARETTO_EvaluateTestSet.Rd
75d9309f6297c43e113eef4acaee6d36 *man/AMARETTO_ExportResults.Rd
7b4ed54d44c6853c6eddf16223af8228 *man/AMARETTO_HTMLreport.Rd
298006ccf620bce03e9e2de18c710dae *man/AMARETTO_Initialize.Rd
ded0dd61bd9881732d4b219864aa7b86 *man/AMARETTO_LarsenBased.Rd
707cc0f948e193bd3b3e7613c38d046c *man/AMARETTO_LearnRegulatoryProgramsLarsen.Rd
749b3ca2643e4cb77a63636f3a2099e4 *man/AMARETTO_Preprocess.Rd
79cf5fda566f45382b495eed315608f9 *man/AMARETTO_ReassignGenesToClusters.Rd
21921ab858891af39dcab80a35f00c73 *man/AMARETTO_Run.Rd
425bdbc64b6a846a227dd15bd8cd4319 *man/AMARETTO_VisualizeModule.Rd
ff3ee0c064cbf7590263307887ffa110 *man/BatchData.Rd
29c076e88e88b6644a94d93558eca74a *man/Beta.NA.Rd
930693757e95f169b1b3ac17650addd9 *man/ComBat_NoFiles.Rd
1c2fd265138ec244ac81c0825c021437 *man/CreateRegulatorData.Rd
82b6970c7e6aa2176ed364dbd2a23134 *man/Driver_Genes.Rd
ba6a657cad6d13f5309b4e38fa4e5ec1 *man/FindTranscriptionallyPredictive_CNV.Rd
146bfdbcbdb98dfd4cb5ed2021413a9e *man/GeneSetDescription.Rd
e7de14f0e95e17bda037f01544f4abe1 *man/GmtFromModules.Rd
234d1a8055017fb23d60ff0a5383b43d *man/HyperGTestGeneEnrichment.Rd
b96e9a6b35bb6339715b87446a03c537 *man/L.Rd
f36fa4363a4e1d47fc755e30d9ff1bdb *man/Lambda_Sequence.Rd
c3e200a7346d02b907904887c7be0702 *man/MsigdbMapping.Rd
109acf323a3c9a131b6a3a2505b36353 *man/Preprocess_MAdata.Rd
18264013e0474bb825b47d7a149ae305 *man/ProcessedDataLIHC.Rd
f2ea2d8fa196c99989a644e29d5aaae7 *man/Save_CancerSite.Rd
382d0601fac092b53304362637c4a4dc *man/TCGA_BatchCorrection_MolecularData.Rd
787d4d1d77c6677128d92e255c4c4a9e *man/TCGA_GENERIC_BatchCorrection.Rd
bca5a384ad8f4738f45c8b0ea459d89c *man/TCGA_GENERIC_CheckBatchEffect.Rd
31f561cb1c670b4abb6ea2a6d31a7c80 *man/TCGA_GENERIC_CleanUpSampleNames.Rd
9e9d11f5d75bdcf4effccd71023533b2 *man/TCGA_GENERIC_GetSampleGroups.Rd
31e07cbd328e81292272b041c17d0c3d *man/TCGA_GENERIC_MergeData.Rd
39c1e397a6728f9d4b660e21cf6e1b55 *man/TCGA_Load_GISTICdata.Rd
ef7c79765726cc1a32040c2cdbd66719 *man/TCGA_Load_MolecularData.Rd
2164aa70f5951e20106fca0c7a4fdfcf *man/aprior.Rd
dc89a8fd8efdc6963a87b37708b9164a *man/bprior.Rd
61b03d663ff1dc31b46107c606aee3c3 *man/build.design.Rd
3d5ef2b4f47526d2cee60df428f1bd54 *man/cacheResource.Rd
2f8da702399641cd147ee35633fc0467 *man/computeGisticURL.Rd
a4fdd5f4194185a3975b159ddc2d53fa *man/design.mat.Rd
d9197219394a7737a5933c9695ef2da8 *man/filter.absent.Rd
9dc0171a9e1d9de7c8cddadcd306e103 *man/geneFiltering.Rd
ce7c3b5e6e30f413f3c4eff568d55ecc *man/get_firehoseData.Rd
87dc52e3e20f05ad87628b5855b50105 *man/int.eprior.Rd
53ce4d8ec5c35a05620ca0a631d13d8e *man/it.sol.Rd
e06d157fd2ebc9c3e1061ed31d858dc3 *man/list.batch.Rd
909a7785c1b01bdd12ce37f9aa88da2c *man/plot_run_history.Rd
8b7f16d1b9b7987b8f9106a8f9e46719 *man/postmean.Rd
b5e254ed3f83c8c343fab932a24680dc *man/postvar.Rd
425c64b8ed06ca6ce0b08894487480ce *man/printf.Rd
32f04c6938dcc5fa98fd0883fe4ac5f5 *man/readGMT.Rd
d1a84e615b8c1b0973383966ea4f3a2f *man/read_gct.Rd
345e0f8d4eba0a3aa851559721452b1e *man/trim.dat.Rd
7127730b0b88a116280409d4e59ae361 *man/write_gct.Rd
7b77fb7514cdd12e0331e8e1a58de2d6 *tests/testthat.R
4d7c0bb00b0856e60879e6253b2a69b7 *tests/testthat/test_AMARETTO.R
26ffc7d48015b8b2c6bf15a06b1edd8d *vignettes/_output.yaml
02a1436195291a1b224eeafea50e1745 *vignettes/_site.yml
8e09f1205bf130ee9474c4bc8ca658e4 *vignettes/amaretto.Rmd
ced3137ec7c43fafa4e62d8ff1989dea *vignettes/include/after_body.html
e92107cb1a3d69ff54afc12fd53c7afb *vignettes/include/before_body.html
d3bef594b1a9608253cb78fb48ff0dce *vignettes/include/header.html
f1aca05645f5afe309344fe3d947c191 *vignettes/include/site.css
