Files in jamesdalg/CNVScope
A Versatile Toolkit for Copy Number Variation Relationship Data Analysis and Visualization
.Rbuildignore
.gitattributes
.github/workflows/R-CMD-check.yaml
.gitignore
CNVScope.Rproj
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/CNVScopeserver.R
R/GRanges_to_underscored_pos.R
R/averageMatrixEdges.R
R/calcCNVKernelProbDist.R
R/calcVecLMs.R
R/createChromosomalMatrixSet.R
R/divisors.R
R/downsample_genomic_matrix.R
R/extractNegLogPval.R
R/formSampleMatrixFromRawGDCData.R
R/freadGDCfile.R
R/getAnnotationMatrix.R
R/getAsymmetricBlockIndices.R
R/getBlockAverageMatrixFromBreakpoints.R
R/getGlobalRescalingStats.R
R/getInterchromosomalInteractivePlot.R
R/importBreakpointBed.R
R/mathead.R
R/nbl_result_matrix_sign_small.R
R/postProcessLinRegMatrix.R
R/rebinGenomicInteractions.R
R/runCNVScopeLocal.R
R/runCNVScopeShiny.R
R/signedRescale.R
R/underscored_pos_to_GRanges.R
R/writeAsymmetricMeltedMatrixToDisk.R
R/writeMeltedChromosomalMatrixToDisk.R
data/nbl_result_matrix_sign_small.rda
doc/additonal_examples.R
doc/additonal_examples.Rmd
doc/additonal_examples.html
doc/create_input_matrix.R
doc/create_input_matrix.Rmd
doc/create_input_matrix.html
doc/create_input_matrix_tcga_prad.R
doc/create_input_matrix_tcga_prad.Rmd
doc/create_input_matrix_tcga_prad.html
doc/create_output_matrix.R
doc/create_output_matrix.Rmd
doc/create_output_matrix.html
doc/power_analysis.R
doc/power_analysis.Rmd
doc/power_analysis.html
docs/.gitattributes
docs/3D_BLCAv2.gif
docs/LICENSE_addendum.txt
docs/README.Rmd
docs/README.html
docs/README.md
docs/_config.yml
docs/blca3d.html
docs/blca_3D.png
docs/chr17_contour_blca.png
docs/chr17_corr_diff_blca.png
docs/chr17_probdist_blca.png
docs/cnvscope_tutorial.mp4
docs/control_panel_demo.gif
docs/create_input_matrix_tcga_prad.Rmd
docs/download_from_cart_prad.png
docs/prad_files.png
docs/tp53_tert_walkthrough.gif
docs/zoomed_tp53_tert.gif
inst/extdata/censushg19.rds
inst/extdata/ensembl_gene_tx_table_prot.rda
inst/extdata/grch37.rda
inst/extdata/nbl_result_matrix_sign_small.rda
inst/extdata/nbl_result_matrix_small.rds
inst/extdata/sample_breakpoints.bed
inst/extdata/sample_breakpoints_chr1.bed
inst/extdata/somaticCnvSegmentsDiploidBeta_TARGET-30-PANRVJ_NormalVsPrimary.tsv
man/CNVScopeserver.Rd
man/GRanges_to_underscored_pos.Rd
man/averageMatrixEdges.Rd
man/calcCNVKernelProbDist.Rd
man/calcVecLMs.Rd
man/createChromosomalMatrixSet.Rd
man/divisors.Rd
man/downsample_genomic_matrix.Rd
man/extractNegLogPval.Rd
man/formSampleMatrixFromRawGDCData.Rd
man/freadGDCfile.Rd
man/getAnnotationMatrix.Rd
man/getAsymmetricBlockIndices.Rd
man/getBlockAverageMatrixFromBreakpoints.Rd
man/getGlobalRescalingStats.Rd
man/getInterchromosomalInteractivePlot.Rd
man/importBreakpointBed.Rd
man/mathead.Rd
man/nbl_result_matrix_sign_small.Rd
man/postProcessLinRegMatrix.Rd
man/rebinGenomicInteractions.Rd
man/runCNVScopeLocal.Rd
man/runCNVScopeShiny.Rd
man/signedRescale.Rd
man/underscored_pos_to_GRanges.Rd
man/writeAsymmetricMeltedChromosomalMatrixToDisk.Rd
man/writeMeltedChromosomalMatrixToDisk.Rd
vignettes/NBL_custom_sample_matched_input_matrix_1e5binsize_parallel.rds
vignettes/NBL_custom_sample_matched_input_matrix_1e7binsize.rds
vignettes/NBL_custom_sample_matched_input_matrix_1e8binsize.rds
vignettes/NBL_custom_sample_matched_input_matrix_2.5e5binsize_parallel.rds
vignettes/NBL_data_files.png
vignettes/NBL_sample_matched_input_matrix.rds
vignettes/additonal_examples.R
vignettes/additonal_examples.Rmd
vignettes/additonal_examples.html
vignettes/aml_sample_matched_input_matrix.rds
vignettes/blca_sample_matched_input_matrix.rds
vignettes/chr11_1e5_nbl.jpg
vignettes/chr11_1e6_nbl.jpg
vignettes/chr11_1e7_nbl.jpg
vignettes/chr11_1e8_nbl.jpg
vignettes/chr11_2.5e5_nbl.jpg
vignettes/chr17_contour_blca.png
vignettes/chr17_corr_diff_blca.png
vignettes/chr17_probdist_blca.png
vignettes/create_input_matrix.R
vignettes/create_input_matrix.Rmd
vignettes/create_input_matrix.html
vignettes/create_output_matrix.R
vignettes/create_output_matrix.Rmd
vignettes/create_output_matrix.html
vignettes/download_from_cart.png
vignettes/nbl_result_matrix_small.rds
vignettes/nbl_slurm_object_test_zero_removed.rds
vignettes/power_analysis.R
vignettes/power_analysis.Rmd
vignettes/power_analysis.html
vignettes/skcm_sample_matched_input_matrix.rds
