87e81a115321a796a1e32cfbb495fdfb *DESCRIPTION
7f86a1c1e8e5bb5533088de51ae0e6cd *LICENSE
145809288e141972a66fb244f64d9bab *NAMESPACE
9c625b4a24f023b997e2f059e2942326 *NEWS.md
e8ac9f40f37ee18fb1ecc3bd6d672e35 *R/CNVScopeserver.R
9deb2f82f164d97c8be810de327ccf36 *R/GRanges_to_underscored_pos.R
90fdf0c988c9a981e5e7bf21ee6a8278 *R/averageMatrixEdges.R
4a9d8025dacd7bcbd4a270ee60ea0a91 *R/calcCNVKernelProbDist.R
d8e0e5aa58a8e7102cb6b542310e595c *R/calcVecLMs.R
a423cca0d0f3a2310eebc4b7b8bdf72b *R/createChromosomalMatrixSet.R
bf5f8b27ef8cfae9e38a36b97be4dac5 *R/downsample_genomic_matrix.R
69482a301c3730b85d65201f1db8f7f0 *R/extractNegLogPval.R
95bf91f385c674ebaa2ea262c65d0d7b *R/formSampleMatrixFromRawGDCData.R
3ebe4d3f5aabceeb471dae8cd438ceab *R/freadGDCfile.R
065155f9bee9dd0726575cf551e123e6 *R/getAnnotationMatrix.R
ada6abb06aee21bb8fdc1d3c1f800bbe *R/getAsymmetricBlockIndices.R
3ca40b27135ce08827c3f41992d34682 *R/getBlockAverageMatrixFromBreakpoints.R
9226ec7f0c459de8b0d3f6138e75636a *R/getGlobalRescalingStats.R
f48df2cf03ed784a118e8177d8d8421c *R/getInterchromosomalInteractivePlot.R
1c10bcd506de81114f93bde43a09beab *R/importBreakpointBed.R
c1a1fbd43ce79bf271c8cbcc3250dfe3 *R/mathead.R
a382ed970526d0ce9890db957024ef4b *R/nbl_result_matrix_sign_small.R
0d49fcd927473cc6447749937025f8db *R/postProcessLinRegMatrix.R
8c9fb0520960a8666e1f05d2848af8c5 *R/rebinGenomicInteractions.R
aec716c9edb7ffe554bbb11a88feaa7a *R/runCNVScopeLocal.R
2bc6190425fadf99d306d5813fa4b975 *R/runCNVScopeShiny.R
73f13e34fa2759548794a5c4e6cf8a63 *R/signedRescale.R
fd8253315e8ca27731ae50d87a2d159e *R/underscored_pos_to_GRanges.R
af199c85ee585921da3c9242e7bd2b53 *R/writeAsymmetricMeltedMatrixToDisk.R
ae9e6d989648751505ec9ae4dbbc2bb0 *R/writeMeltedChromosomalMatrixToDisk.R
c83ee39760821047ddbaee1994434869 *build/vignette.rds
aeda73c6819b4732a2a66290d06dcbdb *data/nbl_result_matrix_sign_small.rda
9d01031b7de2015bc4e348dee2990152 *inst/doc/additonal_examples.R
b786f9fe73c9cf59f658c7a4a618af5f *inst/doc/additonal_examples.Rmd
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faac5e9af01acc77e7ccdcb76d3a58f3 *inst/doc/create_input_matrix.R
1af1c9c67f1892a9f5b004f54a95e059 *inst/doc/create_input_matrix.Rmd
28e875e893e312502fdd4f54ebf1c6a5 *inst/doc/create_input_matrix.html
13e983753963dd9c099939c4dd8a8cfd *inst/doc/create_output_matrix.R
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56f478193f0b892a44d3898f0226e25c *inst/doc/power_analysis.R
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7ed74d8cb4dd818d596514e25eca53bb *inst/extdata/censushg19.rds
5a0219514df373ed430ebcfa20bb30ad *inst/extdata/ensembl_gene_tx_table_prot.rda
c18d24695cfa463fb5a9b867793b9c33 *inst/extdata/grch37.rda
aeda73c6819b4732a2a66290d06dcbdb *inst/extdata/nbl_result_matrix_sign_small.rda
a9e478254424c4b4a051f8d1730f909c *inst/extdata/nbl_result_matrix_small.rds
8ed4a29f37ba2ccb81c3ca433ad84707 *inst/extdata/sample_breakpoints.bed
9eefde13d3be21a8b8bd2277c3f03a79 *inst/extdata/sample_breakpoints_chr1.bed
578ea4e683719300902c33e4fc9dfbfb *inst/extdata/somaticCnvSegmentsDiploidBeta_TARGET-30-PANRVJ_NormalVsPrimary.tsv
e737be5cadbd0310edb8e9591d6a4227 *man/CNVScopeserver.Rd
9fdcd13c36b5d039c6a7fbedbf9068c8 *man/GRanges_to_underscored_pos.Rd
de139c8f97264e7236722357c9bc1485 *man/averageMatrixEdges.Rd
df67aebebac237a63f02a2b3273f606c *man/calcCNVKernelProbDist.Rd
5dcee8077fdf7908ccd119b801d525bb *man/calcVecLMs.Rd
f986c97ef4942dd2c7d20a0bb7e0699d *man/createChromosomalMatrixSet.Rd
1959bc98deedee03f5c6def711a9bbcc *man/downsample_genomic_matrix.Rd
70d8b7f94323d6376a522db98b30cf32 *man/extractNegLogPval.Rd
07e1508c9876f7f3e7fbb7ab9a193b32 *man/formSampleMatrixFromRawGDCData.Rd
74c91f29ef9c3a4aa18711862fad4a27 *man/freadGDCfile.Rd
0f877168a13b8cdb8597f80faf377b2c *man/getAnnotationMatrix.Rd
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18cb8fa8ae978b793a86427fd027b509 *man/getGlobalRescalingStats.Rd
909e753db43a5eab2e69d69b037f062c *man/getInterchromosomalInteractivePlot.Rd
cdccb59b9a4e15b142ddb7168cd55d5c *man/importBreakpointBed.Rd
ce548c6787142e1b106d9a53d3a8045b *man/mathead.Rd
236610841edb071e9c8f64c6472204c6 *man/nbl_result_matrix_sign_small.Rd
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0f88ae74f5eb7b14e8913ec1d185b094 *man/runCNVScopeLocal.Rd
8f088cd49e1f593f8d859d6debfab20f *man/runCNVScopeShiny.Rd
69bb5e71f9b070853610851fbdebdc26 *man/signedRescale.Rd
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325f2027a80a9d50b9bf3eae71f13b10 *man/writeAsymmetricMeltedChromosomalMatrixToDisk.Rd
0abdbc895b7b3f155b51de869762382b *man/writeMeltedChromosomalMatrixToDisk.Rd
7fc5db8f94b5ecfbc0dd7fb945e70687 *vignettes/NBL_custom_sample_matched_input_matrix_1e5binsize_parallel.rds
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c219e11db786238b9bb6d91f25f57a87 *vignettes/NBL_sample_matched_input_matrix.rds
b786f9fe73c9cf59f658c7a4a618af5f *vignettes/additonal_examples.Rmd
e6a4ba99492fe5c8afa102120a8249a7 *vignettes/aml_sample_matched_input_matrix.rds
a37f64db7c072fae260763ea2b0424ac *vignettes/blca_sample_matched_input_matrix.rds
7e0f90ee65364ae4533e044acba5c615 *vignettes/chr11_1e5_nbl.jpg
bc64ba0e9653eb5a47e678ec9b0b6f9f *vignettes/chr11_1e6_nbl.jpg
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eab695593d348fc34449881f6855fe73 *vignettes/chr17_contour_blca.png
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10340b6f9459af6d458557af8c1c9ba1 *vignettes/power_analysis.Rmd
55c803d38d4591a66b61591854c17594 *vignettes/skcm_sample_matched_input_matrix.rds
