Files in uclahs-cds/public-R-NanoStringNormCNV
Helper Functions to Normalize NanoString CNV Data
.Rbuildignore
.cicd-env
.github/workflows/R-CMD-check.yaml
.github/workflows/static-analysis.yml
.gitignore
DESCRIPTION
LICENSE.md
NAMESPACE
NEWS
R/apply.kd.cna.thresh.R
R/apply.ns.cna.thresh.R
R/calculate.replicate.concordance.R
R/calculate.replicate.variance.R
R/call.cnas.with.matched.normals.R
R/call.cnas.with.pooled.normals.R
R/call.copy.number.values.R
R/collapse.genes.R
R/evaluate.replicates.R
R/generate.plot.covariates.R
R/generate.plot.legend.R
R/get.ari.R
R/get.cna.thresholds.R
R/get.tumour.normal.ratio.R
R/invariant.probe.norm.R
R/load.phenodata.R
R/make.cna.densities.plots.R
R/make.cna.heatmap.R
R/make.counts.heatmap.R
R/make.invariant.probe.plot.R
R/make.positive.control.plot.R
R/make.restriction.fragmentation.plot.R
R/make.sample.correlations.heatmap.R
R/normalize.global.R
R/normalize.per.chip.R
R/positive.control.qc.R
R/process.xy.probes.R
R/restriction.fragmentation.qc.R
R/tumour.normal.ratio.to.cn.state.R
R/visualize.results.R
README.md
data/NanoString.DNA.norm.rda
data/NanoString.DNA.raw.rda
data/PhenoData.rda
data/datalist
inst/doc/NanoStringNormCNV_Introduction.R
inst/doc/NanoStringNormCNV_Introduction.Rnw
inst/doc/NanoStringNormCNV_Introduction.pdf
inst/extdata/PhenoData.tsv
inst/tests/data/postive.control.norm.expect.txt
inst/tests/data/sample1.RCC
inst/tests/data/sample2.RCC
inst/tests/test.positive.control.norm.R
man/NanoString.DNA.norm.Rd
man/NanoString.DNA.raw.Rd
man/PhenoData.Rd
man/apply.kd.cna.thresh.Rd
man/apply.ns.cna.thresh.Rd
man/calculate.replicate.concordance.Rd
man/calculate.replicate.variance.Rd
man/call.cnas.with.matched.normals.Rd
man/call.cnas.with.pooled.normals.Rd
man/call.copy.number.values.Rd
man/collapse.genes.Rd
man/evaluate.replicates.Rd
man/generate.plot.covariates.Rd
man/generate.plot.legend.Rd
man/get.ari.Rd
man/get.cna.thresholds.Rd
man/get.tumour.normal.ratio.Rd
man/invariant.probe.norm.Rd
man/load.phenodata.Rd
man/make.cna.densities.plots.Rd
man/make.cna.heatmap.Rd
man/make.counts.heatmap.Rd
man/make.invariant.probe.plot.Rd
man/make.positive.control.plot.Rd
man/make.restriction.fragmentation.plot.Rd
man/make.sample.correlations.heatmap.Rd
man/normalize.global.Rd
man/normalize.per.chip.Rd
man/positive.control.qc.Rd
man/process.xy.probes.Rd
man/restriction.fragmentation.qc.Rd
man/tumour.normal.ratio.to.cn.state.Rd
man/visualize.results.Rd
metadata.yaml
tests/run-all.R
vignettes/NanoStringNormCNV_Introduction.Rnw
vignettes/all-invariant-probe-counts_scatterplot.png
vignettes/low-invariant-probe-counts_barplot.png
vignettes/norm-count_inter-sample-correlation-heatmap.png
vignettes/normalized-logged_counts-heatmap.png
vignettes/positive-control-correlations_zoomed-in.png
vignettes/raw-cna-calls_cna-heatmap.png
vignettes/raw-cna-calls_gene-densityplot.png
vignettes/raw-cna-calls_sample-densityplot.png
vignettes/raw-cna-calls_sample-logged-densityplot.png
vignettes/raw-count_inter-sample-correlation-heatmap.png
vignettes/raw-logged_counts-heatmap.png
vignettes/replicate_cna-calls_cna-heatmap.png
vignettes/replicate_cna-concordance_counts-heatmap.png
vignettes/replicate_norm-count_inter-sample-correlation-heatmap.png
vignettes/replicate_norm-logged_counts-heatmap.png
vignettes/replicate_raw-logged_counts-heatmap.png
vignettes/replicate_tumour-only_norm-count_inter-sample-correlation-heatmap.png
vignettes/restriction-fragmentation-ratios_multiplot.png
vignettes/restriction-fragmentation-ratios_multiplot_all.png
vignettes/rounded-cna-calls_cna-heatmap.png
vignettes/rounded-cna-calls_gene-densityplot.png
vignettes/rounded-cna-calls_sample-densityplot.png
