981692fda64d6bedacdb95f8aebb0303 *DESCRIPTION
bdf32c98d74e02898b8558ebe90844e1 *LICENSE
3c89aa49a91b0e763f3e96c5d6d534e5 *NAMESPACE
0dd83dd784a736412e773f6d039a6262 *R/CNVScopeserver.R
63bb426f56867e1391004a5529a173f1 *R/GRanges_to_underscored_pos.R
51e6b94df226e518062600b742515c4f *R/averageMatrixEdges.R
8a71cd32563989232d2b719f4fe9f568 *R/calcCNVKernelProbDist.R
cfeb7bb5ae25d82722ec9dac0d353471 *R/calcVecLMs.R
59af4ed939a5082c334eed65904d8fd7 *R/createChromosomalMatrixSet.R
ac88e22ece009215f10286b102ed12e6 *R/downsample_genomic_matrix.R
5e3fbd0abc98f1d06f2233e3b6a5486c *R/extractNegLogPval.R
5aa430bf32017408f9f0ef2467d5d1b1 *R/formSampleMatrixFromRawGDCData.R
ffd57e83618f072f7ede233ce4af01ae *R/freadGDCfile.R
f419f997d672557b35e8d9542cfd2510 *R/getAnnotationMatrix.R
c5f2fc4fd2ab49c068c0730c1849735b *R/getAsymmetricBlockIndices.R
99c2ce5ab3315733ef2d31be4249c8dd *R/getBlockAverageMatrixFromBreakpoints.R
608982bbeb7fe166250ca5f6f802236f *R/getGlobalRescalingStats.R
8ab9dec7d322d5d98e2c1c2e2b14e6c0 *R/getInterchromosomalInteractivePlot.R
5c55c95a5eed8ed452cf8f67448d775a *R/importBreakpointBed.R
c9fd6da6cb7e518eee4ecdcaefdd14e5 *R/mathead.R
408b5db928dc2bf04c4999c0e9dd20ef *R/nbl_result_matrix_sign_small.R
443c286ffb511d67ba84952904513958 *R/postProcessLinRegMatrix.R
cdae2f1545969091d0eb81de9aff4e8b *R/rebinGenomicInteractions.R
dcb801b84eb6ac2bf486b8a7fd67497e *R/runCNVScopeShiny.R
cccfa9511d78a96bf9d48af6a08ca83a *R/signedRescale.R
307cecabf0efdf0b146bca2aac1c2edc *R/underscored_pos_to_GRanges.R
76ac3c285f420efc682ec782e8bd02c8 *R/writeAsymmetricMeltedMatrixToDisk.R
3d6c729c63dafe99c937b63c0001cca4 *R/writeMeltedChromosomalMatrixToDisk.R
cc7ae3d0aa2d83066f47327b8edd3ec5 *build/vignette.rds
aeda73c6819b4732a2a66290d06dcbdb *data/nbl_result_matrix_sign_small.rda
af80db6e513b624c8239c2405e31cd08 *inst/doc/create_input_matrix.R
bf3369bf987eb9897909174c3f3248c5 *inst/doc/create_input_matrix.Rmd
ec6f5d42251784d76354b72fbc89b811 *inst/doc/create_input_matrix.html
a45c6d682d3e80a4f767169c1cf09b78 *inst/doc/create_output_matrix.R
ea0a82c3c6e77ac5aa5ef9354db4848d *inst/doc/create_output_matrix.Rmd
4909ed56836c30dd6ad329317dd9b4ce *inst/doc/create_output_matrix.html
0c87a8affd3c435402fe31731b21f341 *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
8e2d8e279d991793d2eae5cbd8c28cb1 *inst/extdata/sample_breakpoints.bed
e58d34523c28a8e93d06f0c52101c134 *inst/extdata/sample_breakpoints_chr1.bed
578ea4e683719300902c33e4fc9dfbfb *inst/extdata/somaticCnvSegmentsDiploidBeta_TARGET-30-PANRVJ_NormalVsPrimary.tsv
7b2ba9daba6b83ba1e693806a7841eb2 *man/CNVScopeserver.Rd
2b7c88e2702e0272047c7f11a06e66c1 *man/GRanges_to_underscored_pos.Rd
c6824896922d461e3367c46369f096ec *man/averageMatrixEdges.Rd
f0b98c27ceda8c4ab29c078ae9764aa2 *man/calcCNVKernelProbDist.Rd
ab72298ae05c017aa6b2d4e45d53d862 *man/calcVecLMs.Rd
86f45e07a367b2499d1edbdbde3d6bce *man/createChromosomalMatrixSet.Rd
34e93c1e485990902658171362fd048b *man/downsample_genomic_matrix.Rd
ef6da51cc556af8110d778d0d7ccb6a8 *man/extractNegLogPval.Rd
bd8dc1c09cef620d618d8e378c1b7c40 *man/formSampleMatrixFromRawGDCData.Rd
8b44c984ef60a5bb30728ebfbbdab378 *man/freadGDCfile.Rd
f184d8f927471653648e5a338f39307d *man/getAnnotationMatrix.Rd
f96b6f7e9438cf0296d757354da3537b *man/getAsymmetricBlockIndices.Rd
1f8e5b67914d4360e6fdf9476580b8d2 *man/getBlockAverageMatrixFromBreakpoints.Rd
d0b42a159b530b641bfad54cdb70317e *man/getGlobalRescalingStats.Rd
8cd19161a7c3aab13a826ecbf9b17db4 *man/getInterchromosomalInteractivePlot.Rd
0a996afe8fe724796da9bfeed63ffc1a *man/importBreakpointBed.Rd
ac5cc8d0d29885c918752ff926bad70e *man/mathead.Rd
08bdb9897b2f10083adfde111eaf9d63 *man/nbl_result_matrix_sign_small.Rd
89ec767531d5d32de286e5ddd1f84560 *man/postProcessLinRegMatrix.Rd
6fd5ea6bd7e7ec1407a657d09e81ac66 *man/rebinGenomicInteractions.Rd
b2a13b91c1eeaca3b1e266aebaefbb52 *man/runCNVScopeShiny.Rd
7cf0d8b07e3f4f703a82999fa6e31d3c *man/signedRescale.Rd
cb87df6c46ce2f4d635a471290c54ddd *man/underscored_pos_to_GRanges.Rd
0c495f229aebbfed8e7e4a651858ecd6 *man/writeAsymmetricMeltedChromosomalMatrixToDisk.Rd
95d7d695e5be0ab1ff3f447682f4aedf *man/writeMeltedChromosomalMatrixToDisk.Rd
3e9d1e1609f214066eeeaf96834a1965 *vignettes/NBL_data_files.png
c219e11db786238b9bb6d91f25f57a87 *vignettes/NBL_sample_matched_input_matrix.rds
bf3369bf987eb9897909174c3f3248c5 *vignettes/create_input_matrix.Rmd
ea0a82c3c6e77ac5aa5ef9354db4848d *vignettes/create_output_matrix.Rmd
84824ab02509dc11717975fdc1a3b0e5 *vignettes/download_from_cart.png
341363c2e60976c908cd381ddd8b4271 *vignettes/interchromosomal_view.png
a9e478254424c4b4a051f8d1730f909c *vignettes/nbl_result_matrix_small.rds
1d176255f8cd79c42ff9bf48538201f8 *vignettes/nbl_slurm_object_test_zero_removed.rds
