Files in qPLEXanalyzer
Tools for qPLEX-RIME data analysis
NEWS
NAMESPACE
DESCRIPTION
R/pcaPlot.R
R/peptideIntensityPlot.R
R/assignColours.R
R/normalizeQuantiles.R
R/mergePeptides.R
R/corrPlot.R
R/checkArguments.R
R/intensityBoxplot.R
R/regressIntensity.R
R/coveragePlot.R
R/getContrastResults.R
R/convertToMSnset.R
R/rliPlot.R
R/hierarchicalPlot.R
R/rowScaling.R
R/qPLEXanalyzer-package.R
R/groupScaling.R
R/intensityPlot.R
R/summarizeIntensities.R
R/computeDiffStats.R
R/normalizeScaling.R
R/plotMeanVar.R
R/maVolPlot.R
inst/CITATION
inst/doc/qPLEXanalyzer.R
inst/doc/qPLEXanalyzer.Rmd
inst/doc/qPLEXanalyzer.html
inst/extdata/P03372.fasta
build/vignette.rds
tests/testthat.R
tests/testthat/test-assignColours.R
tests/testthat/test-regressIntensity.R
tests/testthat/test-intensityPlot.R
tests/testthat/test-getContrastResults.R
tests/testthat/getContrastResults.rds
tests/testthat/test-convertToMSnSet.R
tests/testthat/test-summarizeIntensity.R
tests/testthat/regressIntensities.rds
tests/testthat/test-normalizeQuantiles.R
tests/testthat/normalizeQuantiles.rds
tests/testthat/summarizeIntensities.rds
tests/testthat/mergePeptides_phos.rds
tests/testthat/convertToMSnset_phospho_msnset.rds
tests/testthat/assignColours_rep.rds
tests/testthat/test-groupScaling.R
tests/testthat/test-computeDiffStats.R
tests/testthat/test-hierarchicalPlot.R
tests/testthat/normalizeScaling_prot.rds
tests/testthat/test-peptideIntensityPlot.R
tests/testthat/test-rliPlot.R
tests/testthat/test-rowScaling.R
tests/testthat/test-mergePeptides.R
tests/testthat/rowScaling.rds
tests/testthat/normalizeScaling.rds
tests/testthat/test-coveragePlot.R
tests/testthat/groupScaling.rds
tests/testthat/test-normalizeScaling.R
tests/testthat/test-maVolPlot.R
tests/testthat/test-pcaPlot.R
tests/testthat/test-corrPlot.R
tests/testthat/computeDiffStats.rds
tests/testthat/mergePeptides.rds
tests/testthat/test-intensityBoxplot.R
tests/testthat/assignColours_sg.rds
tests/figs/deps.txt
tests/figs/rli-plot/rli-plot-custom-colours.svg
tests/figs/rli-plot/rli-plot.svg
tests/figs/rli-plot/rli-plot-colour-by-biorep-include-igg.svg
tests/figs/hierarchical-plot/hierarchical-plot-veritcal.svg
tests/figs/hierarchical-plot/hierarchical-plot-custom-colour.svg
tests/figs/hierarchical-plot/hierarchical-plot-colour-by-rep.svg
tests/figs/hierarchical-plot/hierarchical-plot.svg
tests/figs/intensity-boxplot/intensity-boxplot-colour-by-rep.svg
tests/figs/intensity-boxplot/intensity-boxplot-custom-colour.svg
tests/figs/intensity-boxplot/intensity-boxplot.svg
tests/figs/peptide-intensity-plot/no-combined-intensity.svg
tests/figs/peptide-intensity-plot/standard.svg
tests/figs/peptide-intensity-plot/with-selected-modification.svg
tests/figs/peptide-intensity-plot/with-selected-sequence.svg
tests/figs/pca-plot/pca-plot-custom-colours-and-pc2-v-pc3.svg
tests/figs/pca-plot/pca-plot.svg
tests/figs/pca-plot/pca-plot-colour-by-biorep-omit-igg.svg
tests/figs/ma-and-volcano-plots/volcano-plot.svg
tests/figs/ma-and-volcano-plots/volcano-plot-with-selected-genes.svg
tests/figs/ma-and-volcano-plots/ma-plot.svg
tests/figs/coverage-plot/coverage-plot-era.svg
tests/figs/correlation-plot/correlation-plot-yellow-to-pink.svg
tests/figs/correlation-plot/correlation-plot-change-limit.svg
tests/figs/correlation-plot/correlation-plot-default-colour.svg
tests/figs/correlation-plot/correlation-plot-default-colour-no-numbers.svg
tests/figs/intensity-density-plot/intensity-density-plot-custom-colour.svg
tests/figs/intensity-density-plot/intensity-density-plot-colour-by-rep.svg
tests/figs/intensity-density-plot/intensity-density-plot.svg
vignettes/qPLEXanalyzer.Rmd
vignettes/library.bib
data/datalist
data/exp3_OHT_ESR1.RData
data/exp2_Xlink.RData
data/mouse_anno.RData
data/human_anno.RData
man/corrPlot.Rd
man/normalizeScaling.Rd
man/maVolPlot.Rd
man/assignColours.Rd
man/rliPlot.Rd
man/intensityPlot.Rd
man/normalizeQuantiles.Rd
man/rowScaling.Rd
man/pcaPlot.Rd
man/peptideIntensityPlot.Rd
man/exp3_OHT_ESR1.Rd
man/hierarchicalPlot.Rd
man/computeDiffStats.Rd
man/groupScaling.Rd
man/convertToMSnset.Rd
man/coveragePlot.Rd
man/intensityBoxplot.Rd
man/getContrastResults.Rd
man/human_anno.Rd
man/plotMeanVar.Rd
man/summarizeIntensities.Rd
man/exp2_Xlink.Rd
man/mergePeptides.Rd
man/regressIntensity.Rd
man/qPLEXanalyzer-package.Rd
