Files in ChenMengjie/SynthEx

A synthetic normal approach to call CNAs from sequencing data.

.Rbuildignore

.gitignore

.travis.yml

DESCRIPTION

Docker/Dockerfile

Docker/Rprofile.site

Docker/SynthEx.R

ExampleFiles/TCGA-A7-A26G.freebayes.vcf

ExampleFiles/TCGA-A7-A26G.normal.bed

ExampleFiles/TCGA-A7-A26G.tumor.bed

ExampleFiles/multiple.normal.samples.bed

LICENSE.txt

NAMESPACE

R/CallWholeGenomeDoubling.R R/Lookup.R R/SynEx-internal.R R/SynthExPipeline.R R/SynthExUserGuide.R R/SynthExcorrectBias.R R/WGS_calratio.R R/WGS_normalization.R R/calratioWGS.R R/chromosomeView.R R/correctBias.R R/correctBypurity.R R/createBins.R R/createCentromereBins.R R/createSegments.R R/createTargetBins.R R/create_synthetic_library.R R/create_synthetic_normal.R R/denoise.R R/groupCNplots.R R/larsCBSsegment.R R/merge_synthetic_library.R R/normalization.R R/purityEstimate.R R/singleCNreport.R R/synthetic_WGS_ratio.R R/synthetic_correctBias_allpossibility.R R/synthetic_correctBias_allsamples.R R/synthetic_correctBias_nearsamples.R R/synthetic_nearsamples_WGS_calratio.R README.md

SynthEx.Rproj

data/CentromereAnnotations.rda

data/TCGAbreast.rda

data/TargetAnnotations.rda

data/datalist

inst/doc/SynthExUserGuide.pdf

inst/doc/freebayes_to_bed.py

vignettes/SynthEx-knitr.Rnw

vignettes/SynthEx-knitr.pdf

vignettes/figure/fig1-1.png

vignettes/figure/fig2-1.png

vignettes/figure/heatmap-1.png

vignettes/figure/heatmap2-1.png

vignettes/figure/multiple1-1.jpg

vignettes/figure/multiple2-1.jpg

vignettes/figure/normalization-1.png

vignettes/figure/purity-1.png

vignettes/figure/seg1-1.png

ChenMengjie/SynthEx documentation built on Oct. 1, 2020, 8:45 a.m.