Files in lizamathews/CAISC
Clonal Architecture with Integration of SNV and CNV
.DS_Store
.gitattributes
DESCRIPTION
NAMESPACE
R/DENDRO_functions.R
R/cnv_distance_matrix.R
R/complex_heatmap.R
R/integration.R
R/snv_distance_matrix.R
README.md
data/DENDRO_input_10mutations.rda
data/cnvSimulation.r
data/cnv_matrix.RDS
data/integrated_matrix.RDS
data/sampleID.rda
data/sample_heatmap.RDS
data/sample_vcf.rda
data/simulation_Dataset.r
data/snv_matrix.RDS
figures/SampleHeatmapMGH28_29.png
figures/figure1.jpg
inst/extdata/GSE57872_merged.vcf.zip
inst/extdata/SRR_ID.txt
inst/extdata/annotationCell_28_29.txt
inst/extdata/annotationGene_28_29.txt
inst/extdata/temp.rtf
man/EntropytoALPHA.Rd
man/calculateEntropy.Rd
man/calculateEntropyMatrix.Rd
man/calculateEntropyMatrixAllEdge.Rd
man/createCNVMatrix.Rd
man/createComplexHeatmap.Rd
man/createIntegratedMatrix.Rd
man/createSNVMatrix.Rd
man/makeInferCNVObject.Rd
man/vcf_to_SNVinput.Rd
script/GATKpipeline.sh
script/filter_vcf_mutation.pl
script/filter_vcf_mutation_5.pl.txt
script/merge_vcfs.sh
script/sample_pipeline.R
script/scriptDownload.sh
script/scriptFASTQ_1.sh
script/vcf_to_DENDROinputMerged.R
vignette/vignette.Rmd
vignette/vignette.html
