040b32a983b22c64e51ef9955d88da65 *DESCRIPTION
7f86a1c1e8e5bb5533088de51ae0e6cd *LICENSE
bd330bf923d3f42ead1accdacec6f536 *NAMESPACE
b02298245d1343033429de142c9e0a21 *NEWS.md
e2e0a07ba15f4f3fce59f6c24f968f81 *R/CNVScopeserver.R
e014011970fef04acf99d2692a4d745a *R/GRanges_to_underscored_pos.R
90fdf0c988c9a981e5e7bf21ee6a8278 *R/averageMatrixEdges.R
106dc19e945c998e5c9f0925b87fe581 *R/calcCNVKernelProbDist.R
6d8dcd8f12ff254f3a54b5d596b61af3 *R/calcVecLMs.R
19be0e07341e2f5cb912248e3cfc1a28 *R/createChromosomalMatrixSet.R
c9791822261d722c6a99aa644b06c49f *R/divisors.R
f62051519fd8b29f20500bfac7ccba54 *R/downsample_genomic_matrix.R
69482a301c3730b85d65201f1db8f7f0 *R/extractNegLogPval.R
60e6d6aaebe2f4b1cd3134885ed81ec9 *R/formSampleMatrixFromRawGDCData.R
494d358523fa3b00054a6e4e0acaf779 *R/freadGDCfile.R
fda4d1ee81ec16825022a686ac799803 *R/getAnnotationMatrix.R
fc7355eb3666c418229c90a80df8b652 *R/getAsymmetricBlockIndices.R
bae29286a6aa87b12f4f5bc9d9744f92 *R/getBlockAverageMatrixFromBreakpoints.R
9226ec7f0c459de8b0d3f6138e75636a *R/getGlobalRescalingStats.R
2d286fe5f86c01be247885ea490b9502 *R/getInterchromosomalInteractivePlot.R
ab965c9700e1a7a36b71f31e5f6d5f43 *R/importBreakpointBed.R
c1a1fbd43ce79bf271c8cbcc3250dfe3 *R/mathead.R
a382ed970526d0ce9890db957024ef4b *R/nbl_result_matrix_sign_small.R
fe0b9fdae3cfa1a1ab7fc47c01780c06 *R/postProcessLinRegMatrix.R
95488bf958dcced7bcf387a994d7b364 *R/rebinGenomicInteractions.R
aec716c9edb7ffe554bbb11a88feaa7a *R/runCNVScopeLocal.R
64f3f743c6c1cc2b5be46601e2eba9b2 *R/runCNVScopeShiny.R
d50f053283c768e282010a4ca89eaa98 *R/signedRescale.R
1a901aa07356168f6816aa612eaff74c *R/underscored_pos_to_GRanges.R
319ad0b74502cee3063eed275e90958a *R/writeAsymmetricMeltedMatrixToDisk.R
8f3b36f107dd2b6b1071e468fd5f8f6c *R/writeMeltedChromosomalMatrixToDisk.R
809433d6c4a143c1f5246b58e953aca9 *build/vignette.rds
6edd728bbea3ff250c291276d830c3d8 *data/nbl_result_matrix_sign_small.rda
02cf0389d5dbb115622fd1d666d115a1 *inst/doc/additonal_examples.R
a80b30db4640e3dbd8775c0c96618376 *inst/doc/additonal_examples.Rmd
4f6b939838656b299a85cc9ea3abf689 *inst/doc/additonal_examples.html
ae830fcebc94655db53adaa060e825e3 *inst/doc/create_input_matrix.R
d4cbff6b03f440b05b777133d4e472c8 *inst/doc/create_input_matrix.Rmd
0336a3644bbf781ff88696ae7c733ff6 *inst/doc/create_input_matrix.html
fc4745837e6933a59ecb1c9d39617b7c *inst/doc/create_output_matrix.R
d1ef7a01d4c8db93170c307bc3e349e5 *inst/doc/create_output_matrix.Rmd
0e6d9ef08138ddcd403ebf28b73985c8 *inst/doc/create_output_matrix.html
5d2cc47c62824c3957b76403550e09e8 *inst/doc/power_analysis.R
520f58389135c4d0f677c9c98ebe489b *inst/doc/power_analysis.Rmd
3f82df194c7dc71a1efc5a80a2033ad9 *inst/doc/power_analysis.html
7ed74d8cb4dd818d596514e25eca53bb *inst/extdata/censushg19.rds
16c0a5136d2cea276e998cb29cfce2e6 *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
aa072ff1059c23cf6915adfa953d9cc5 *man/calcVecLMs.Rd
f986c97ef4942dd2c7d20a0bb7e0699d *man/createChromosomalMatrixSet.Rd
b06961b229cd53edd38e5bf47e9215fa *man/divisors.Rd
1959bc98deedee03f5c6def711a9bbcc *man/downsample_genomic_matrix.Rd
70d8b7f94323d6376a522db98b30cf32 *man/extractNegLogPval.Rd
07e1508c9876f7f3e7fbb7ab9a193b32 *man/formSampleMatrixFromRawGDCData.Rd
74c91f29ef9c3a4aa18711862fad4a27 *man/freadGDCfile.Rd
0f877168a13b8cdb8597f80faf377b2c *man/getAnnotationMatrix.Rd
521d54e90b3fbff73b5f1ca1c92e8193 *man/getAsymmetricBlockIndices.Rd
952c05663996853395b895948b92272c *man/getBlockAverageMatrixFromBreakpoints.Rd
18cb8fa8ae978b793a86427fd027b509 *man/getGlobalRescalingStats.Rd
909e753db43a5eab2e69d69b037f062c *man/getInterchromosomalInteractivePlot.Rd
5073681996c532bf58d455ac42a861a1 *man/importBreakpointBed.Rd
ce548c6787142e1b106d9a53d3a8045b *man/mathead.Rd
236610841edb071e9c8f64c6472204c6 *man/nbl_result_matrix_sign_small.Rd
aa3e16fad9f2c6fcbf6d6be9c72782f3 *man/postProcessLinRegMatrix.Rd
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0f88ae74f5eb7b14e8913ec1d185b094 *man/runCNVScopeLocal.Rd
8f088cd49e1f593f8d859d6debfab20f *man/runCNVScopeShiny.Rd
69bb5e71f9b070853610851fbdebdc26 *man/signedRescale.Rd
33d70f2baa5946cb55e3284bd1280906 *man/underscored_pos_to_GRanges.Rd
325f2027a80a9d50b9bf3eae71f13b10 *man/writeAsymmetricMeltedChromosomalMatrixToDisk.Rd
0abdbc895b7b3f155b51de869762382b *man/writeMeltedChromosomalMatrixToDisk.Rd
0b2f0b040a7118a40a3d43242bd6cc91 *vignettes/NBL_custom_sample_matched_input_matrix_1e5binsize_parallel.rds
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f9f9e489acd8cb5b353f458019cae24c *vignettes/NBL_custom_sample_matched_input_matrix_1e8binsize.rds
6f71055316888eb8249e4c7add00c840 *vignettes/NBL_custom_sample_matched_input_matrix_2.5e5binsize_parallel.rds
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a86a4be27a8492c709a2512a593bc33a *vignettes/NBL_sample_matched_input_matrix.rds
a80b30db4640e3dbd8775c0c96618376 *vignettes/additonal_examples.Rmd
6ffea24c2b405da9b9086a12835773b8 *vignettes/aml_sample_matched_input_matrix.rds
d8f112e96a2d03495ef11f3cd2580317 *vignettes/blca_sample_matched_input_matrix.rds
7e0f90ee65364ae4533e044acba5c615 *vignettes/chr11_1e5_nbl.jpg
bc64ba0e9653eb5a47e678ec9b0b6f9f *vignettes/chr11_1e6_nbl.jpg
cbbfe1bf076cabba735fbdffc03c1dd0 *vignettes/chr11_1e7_nbl.jpg
c8ee016b9eebe6e0db38ec199bf8a9da *vignettes/chr11_1e8_nbl.jpg
2c4755b019cfe6e9de8fdf9a2e023b8a *vignettes/chr11_2.5e5_nbl.jpg
eab695593d348fc34449881f6855fe73 *vignettes/chr17_contour_blca.png
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d4cbff6b03f440b05b777133d4e472c8 *vignettes/create_input_matrix.Rmd
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73168523f4fbef709390f5de7da6b9c0 *vignettes/nbl_result_matrix_small.rds
86bda55a08645008225a311ac10cfd7e *vignettes/nbl_slurm_object_test_zero_removed.rds
520f58389135c4d0f677c9c98ebe489b *vignettes/power_analysis.Rmd
b97bee97e3dad113d64edd0942f2d043 *vignettes/skcm_sample_matched_input_matrix.rds
