Files in PYangLab/PhosR
A set of methods and tools for comprehensive analysis of phosphoproteomics data
.Rapp.history
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yaml
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
PhosR.Rproj
R/Impute.R
R/PhosphoExperiment.R
R/RUVs.R
R/Signalomes.R
R/data.R
R/filter.R
R/getMotifFreq.R
R/getSPS.R
R/kinaseSubstratePrediction.R
R/pathwayAnalysis.R
R/plotFunctions.R
R/plotQC.R
R/toolBox.R
README.md
_pkgdown.yml
data/KinaseFamily.rda
data/KinaseMotifs.rda
data/PhosphoSitePlus.rda
data/SEGs.rda
data/SPSs.rda
data/hSPSs.rda
data/phospho.cells.Ins.pe.rda
data/phospho.cells.Ins.sample.rda
data/phospho.liver.Ins.TC.ratio.RUV.pe.RData
data/phospho_L6_ratio.RData
data/phospho_L6_ratio_pe.rda
data/phospho_liverInsTC_RUV_sample.rda
inst/CITATION
inst/graphical_abstract.png
man/KinaseFamily.Rd
man/PhosphoExperiment-methods.Rd
man/PhosphoExperiment-operate.Rd
man/PhosphoExperiment.Rd
man/PhosphoSite.human.Rd
man/PhosphoSite.mouse.Rd
man/PhosphoSite.rat.Rd
man/RUVphospho.Rd
man/SPSs.Rd
man/Signalomes.Rd
man/createFrequencyMat.Rd
man/figures/PhosR_logo.png
man/frequencyScoring.Rd
man/getSPS.Rd
man/hSEGs.Rd
man/kinaseSubstrateHeatmap.Rd
man/kinaseSubstratePred.Rd
man/kinaseSubstrateProfile.Rd
man/kinaseSubstrateScore.Rd
man/mIntersect.Rd
man/mSEGs.Rd
man/matANOVA.Rd
man/meanAbundance.Rd
man/medianScaling.Rd
man/minmax.Rd
man/motif.human.list.Rd
man/motif.mouse.list.Rd
man/motif.rat.list.Rd
man/pathwayOverrepresent.Rd
man/pathwayRankBasedEnrichment.Rd
man/phosCollapse.Rd
man/phospho.L6.ratio.Rd
man/phospho.L6.ratio.pe.Rd
man/phospho.cells.Ins.Rd
man/phospho.liver.Ins.TC.ratio.RUV.Rd
man/phospho.liver.Ins.TC.ratio.RUV.pe.Rd
man/plotKinaseNetwork.Rd
man/plotQC.Rd
man/plotSignalomeMap.Rd
man/ptImpute.Rd
man/scImpute.Rd
man/selectGrps.Rd
man/selectLocalisedSites.Rd
man/selectOverallPercent.Rd
man/selectTimes.Rd
man/siteAnnotate.Rd
man/standardise.Rd
man/tImpute.Rd
tests/testthat.R
tests/testthat/test-RUVs.R
tests/testthat/test-filter.R
tests/testthat/test-impute.R
tests/testthat/test-pathwayAnalysis.R
tests/testthat/test-plotQC.R
vignettes/PhosR.Rmd
vignettes/web/PhosR_STAR_protocols.html
vignettes/web/PhosR_STAR_protocols2.Rmd
vignettes/web/batch_correction.Rmd
vignettes/web/imputation.Rmd
vignettes/web/pathway_analysis.Rmd
vignettes/web/signalomes.Rmd
vignettes/web/site_gene_analysis.Rmd
