17b48140187f24c6c8bf308137685114 *DESCRIPTION
a635a72df89714aebd2febcce751abf8 *LICENSE
13420185a045af912638d873c2f1c15b *NAMESPACE
5cc9baf3b348048e4c1d2da147354fd2 *NEWS.md
c44f944d83131324eb767c2825a83d05 *R/ELViS.R
8aa080279bb13c38112e1824e88d543b *R/Input_Checking.R
0f3d17a63c337df80fd2869ebac031d0 *R/Plotting.R
8ad6a794b9e0f9935818dd7dbdaeaa03 *R/Process_Bam.R
d45a3845a853f7ea915bbe612a776a71 *R/data.R
0527433c606680267bc739c2f208f97a *R/main.R
e74d07170fc9d71692430c0053bd5fbc *R/misc.R
49b49818097b9dd9ad430c00be22fa71 *README.md
95c06803ce8b223b38ad8fe47af16492 *build/vignette.rds
74527ba16c7ceb5f22b63adfee317dd5 *data/ELViS_toy_run_result.rda
93af42ad492f17c237abda162221047e *data/mtrx_samtools_reticulate.rda
c2cdd7022f591a46b85d128e7bc96f90 *data/total_aligned_base__host_and_virus.rda
36bfe6edea27d372bfb63438a2a46db7 *data/toy_example.rda
ab0f53aa7ee94647c154697c268c4e5d *inst/doc/ELViS_Toy_Example.R
b4cd735a92f5785ca9c6daca06f5a5cc *inst/doc/ELViS_Toy_Example.Rmd
e25cf6efafc17c7e9ff12d25076ef170 *inst/doc/ELViS_Toy_Example.html
73a7c7adc701a95bd60131a18a72cfff *inst/extdata/Control_100X_1102.bam
faaf1616f4e07edd1e269afa1a3803bc *inst/extdata/Control_100X_1102.bam.bai
2bf77bd29ec46ab61f894a921eaa4dbc *inst/extdata/Control_100X_1119.bam
377f666ed34959d6bfdb598afd3039c6 *inst/extdata/Control_100X_1119.bam.bai
08894bb0e5c506aa04ebec6687007ac9 *inst/extdata/HPV16.fa
af50d6d04d2ad26fd422bb10dbfadd15 *inst/extdata/HPV16.fa.fai
3240038b9c83d939c62bf126c3a8bf60 *inst/extdata/HPV16REF_PaVE.gff
aa2176472ed09b757a30260aa14f9080 *inst/scripts/README_extdata.txt
71fc7f1b34bc3c2a6bd6b54ae9cac150 *man/ELViS.Rd
e92457da5cfa341f3f0c0b80f119d2b7 *man/ELViS_toy_run_result.Rd
fe3c1b96dfa4dd70f8779c960bc8cb4e *man/coord_to_grng.Rd
3ca87ec51bb6ab2c7e74e7f2b916aa73 *man/coord_to_lst.Rd
c730c69cc3934d331b964730249a9f5c *man/depth_hist.Rd
2207c9c33bd24bbc9576128381b4d87b *man/filt_samples.Rd
c2dca35356879605ff2617342dfe0292 *man/gene_cn_heatmaps.Rd
176e9cf7b768b408bb06f8e9f4f4bab8 *man/get_depth_matrix.Rd
a8920dd0e0f4be6dfc1bd7f4d256a2c3 *man/get_new_baseline.Rd
2196a091f36de50706dfcf517b2aadf3 *man/integrative_heatmap.Rd
d22ab5dcb9636048ff270b8a6445c650 *man/mtrx_samtools_reticulate.Rd
00954088db0e1efd4f660b5dc5d0637e *man/norm_fun.Rd
db76238f15dc142be68efc30af60c665 *man/plot_pileUp_multisample.Rd
6d982ead251be75111ed54f5742c4c73 *man/run_ELViS.Rd
3333b7a9e1bff0ac201a0030c2494fa2 *man/total_aligned_base__host_and_virus.Rd
10dd141c5e10a09966c2b01b18f04e34 *man/toy_example.Rd
ac93c10feb58b1f95e20696a170eb739 *tests/testthat.R
057fab2afd3c42a8cccaf08bc02af5e0 *tests/testthat/test-Main_Test.R
0d1278509d109b10e6ee77fa107a9be6 *tests/testthat/test-Misc_Test.R
a2e0b0107287ea98605563a59aff805a *tests/testthat/test-Plotting_Test.R
e5d69de3e1e2d3dbafd80f04aeee6258 *tests/testthat/test-Process_Bam_Test.R
89f01b462a7b953880ecd1df02a1fa68 *tests/testthat/test-input_checking.R
b4cd735a92f5785ca9c6daca06f5a5cc *vignettes/ELViS_Toy_Example.Rmd
