Introduction | Installation | Loading packages and data | Setting up the PhosphoExperiment object | Part A. Preprocessing | Imputation | Setting up the data | Filtering of phosphosites | Imputation of phosphosites | Site- and condition-specific imputation | Paired tail-based imputation | Quantification plots | Batch correction | Diagnosing batch effect | Correcting batch effect | Quality control | Generating SPSs | Part B. Downstream analysis | Pathway analysis | 1-dimensional enrichment analysis | Prepare the Reactome annotation | Perform 1D gene-centric pathway analysis | 2- and 3-dimensional signalling pathway analysis | Site- and gene- centric analysis | Gene-centric analyses of the liver phosphoproteome data | Site-centric analyses of the liver phosphoproteome data | Signalomes | Generation of kinase-substrate relationship scores | Signalome construction | Generate signalome map | Generate signalome network | Session Info
Package: PhosR 1.23.0
Di Xiao
PhosR: A set of methods and tools for comprehensive analysis of phosphoproteomics data
PhosR is a package for the comprenhensive analysis of phosphoproteomic data. There are two major components to PhosR: processing and downstream analysis. PhosR consists of various processing tools for phosphoproteomics data including filtering, imputation, normalisation, and functional analysis for inferring active kinases and signalling pathways.
Authors:
PhosR_1.23.0.tar.gz
PhosR_1.23.0.zip(r-4.7)PhosR_1.23.0.zip(r-4.6)PhosR_1.23.0.zip(r-4.5)
PhosR_1.23.0.tgz(r-4.6-any)PhosR_1.23.0.tgz(r-4.5-any)
PhosR_1.23.0.tar.gz(r-4.7-any)PhosR_1.23.0.tar.gz(r-4.6-any)
PhosR_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PhosR/json (API)
| # Install 'PhosR' in R: |
| install.packages('PhosR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- hSEGs - A list of Stably Expressed Genes
- KinaseFamily - KinaseFamily
- motif.human.list - List of human kinase motifs
- motif.mouse.list - List of mouse kinase motifs
- motif.rat.list - List of rat kinase motifs
- mSEGs - A list of Stably Expressed Genes
- phospho.cells.Ins - Phospho.cells.Ins
- phospho.cells.Ins.pe - Phospho.cells.Ins
- phospho.L6.ratio - Phospho.L6.ratio
- phospho.L6.ratio.pe - Phospho_L6_ratio_pe
- phospho.liver.Ins.TC.ratio.RUV - Phospho_liverInsTC_RUV_sample
- phospho.liver.Ins.TC.ratio.RUV.pe - Phospho.liver.Ins.TC.ratio.RUV.pe
- PhosphoSite.human - PhosphoSitePlus annotations for human
- PhosphoSite.mouse - PhosphoSitePlus annotations for mouse
- PhosphoSite.rat - PhosphoSitePlus annotations for rat
- SPSs - A list of Stably Phosphorylated Sites
On BioConductor:PhosR-1.23.0(bioc 3.24)PhosR-1.22.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
softwareresearchfieldproteomics
Last updated from:4fa1a918f8. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 461 | ||
| linux-devel-x86_64 | NOTE | 559 | ||
| source / vignettes | OK | 581 | ||
| linux-release-x86_64 | NOTE | 588 | ||
| macos-release-arm64 | NOTE | 628 | ||
| macos-oldrel-arm64 | NOTE | 291 | ||
| windows-devel | NOTE | 434 | ||
| windows-release | NOTE | 436 | ||
| windows-oldrel | NOTE | 280 | ||
| wasm-release | OK | 266 |
Exports:cbindcreateFrequencyMatfrequencyScoringGeneSymbolGeneSymbol<-getSPSkinaseSubstrateHeatmapkinaseSubstratePredkinaseSubstrateProfilekinaseSubstrateScoreLocalisationLocalisation<-matANOVAmeanAbundancemedianScalingminmaxmIntersectmUnionpathwayOverrepresentpathwayRankBasedEnrichmentphosCollapsePhosphoExperimentplotKinaseNetworkplotQCplotSignalomeMapptImputerbindResidueResidue<-RUVphosphoRUVproteomescImputeselectGrpsselectLocalisedSitesselectOverallPercentselectTimesSequenceSequence<-SignalomesSiteSite<-siteAnnotatestandardisetImputeUniprotIDUniprotID<-
Dependencies:abindbackportsBiobaseBiocGenericsbootbroomcarcarDatacirclizeclassclicodacolorspacecommonmarkcorrplotcowplotcpp11crayoncurlDelayedArraydendextendDerivdoBydplyre1071farverforcatsforecastFormulafracdiffgenericsGenomicRangesGGallyggdendroggplot2ggpubrggrepelggsciggsignifggstatsggtextGlobalOptionsgluegridExtragridtextgtablehmsigraphIRangesisobandjpeglabelinglatticelifecyclelimmalitedownlme4lmtestmagrittrmarkdownMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmgcvminqamodelrnetworknlmenloptrnnetnumDerivpatchworkpbkrtestpcaMethodspheatmappillarpkgconfigplyrpngpolynompreprocessCoreprettyunitsprogressproxypurrrquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasreshape2rlangrstatixruvS4ArraysS4VectorsS7scalesSeqinfoshapeSparseArraySparseMstatmodstatnet.commonstringistringrSummarizedExperimentsurvivaltibbletidyrtidyselecttimeDateurcautf8vctrsviridisviridisLitewithrxfunxml2XVectorzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Create frequency matrix | createFrequencyMat |
| Frequency scoring | frequencyScoring |
| Generate set of stable phosphoporylated sites | getSPS |
| A list of Stably Expressed Genes (SEGs) | hSEGs |
| KinaseFamily | KinaseFamily |
| Kinase-substrate annotation prioritisation heatmap | kinaseSubstrateHeatmap |
| kinaseSubstratePred | kinaseSubstratePred |
| Kinase substrate profiling | kinaseSubstrateProfile |
| Kinase substrate scoring | kinaseSubstrateScore |
| ANOVA test | matANOVA |
| Obtain average expression from replicates | meanAbundance |
| Median centering and scaling | medianScaling |
| Minmax scaling | minmax |
| Multi-intersection, union | mIntersect mUnion |
| List of human kinase motifs | motif.human.list |
| List of mouse kinase motifs | motif.mouse.list |
| List of rat kinase motifs | motif.rat.list |
| A list of Stably Expressed Genes (SEGs) | mSEGs |
| phosphosite/Gene set over-representation analysis | pathwayOverrepresent |
| Phosphosite/Gene set enrichment analysis | pathwayRankBasedEnrichment |
| Summarising phosphosites to proteins | phosCollapse |
| phospho.cells.Ins | phospho.cells.Ins phospho.cells.Ins.pe |
| phospho.L6.ratio | phospho.L6.ratio |
| phospho_L6_ratio_pe | phospho.L6.ratio.pe |
| phospho_liverInsTC_RUV_sample | phospho.liver.Ins.TC.ratio.RUV |
| phospho.liver.Ins.TC.ratio.RUV.pe | phospho.liver.Ins.TC.ratio.RUV.pe |
| The PhosphoExperiment class | coerce, PhosphoExperiment PhosphoExperiment-class PhosphoExperiment-method SummarizedExperiment, |
| PhosphoSitePlus annotations for human | PhosphoSite.human |
| PhosphoSitePlus annotations for mouse | PhosphoSite.mouse |
| PhosphoSitePlus annotations for rat | PhosphoSite.rat |
| Plot kinase network | plotKinaseNetwork |
| A set of function for data QC plot | plotQC |
| Plot signalome map | plotSignalomeMap |
| PhosphoExperiment object accessors | GeneSymbol GeneSymbol,PhosphoExperiment-method GeneSymbol<- GeneSymbol<-,PhosphoExperiment-method Localisation Localisation,PhosphoExperiment-method Localisation<- Localisation<-,PhosphoExperiment-method PPE-accessors Residue Residue,PhosphoExperiment-method Residue<- Residue<-,PhosphoExperiment-method Sequence Sequence,PhosphoExperiment-method Sequence<- Sequence<-,PhosphoExperiment-method Site Site,PhosphoExperiment-method Site<- Site<-,PhosphoExperiment-method UniprotID UniprotID,PhosphoExperiment-method UniprotID<- UniprotID<-,PhosphoExperiment-method |
| PhosphoExperiment object subset, combine methods | cbind cbind,PhosphoExperiment-method PPE-operate rbind rbind,PhosphoExperiment-method [ [,PhosphoExperiment,ANY,ANY,ANY-method [<- [<-,PhosphoExperiment,ANY,ANY,ANY-method |
| Paired-tail (pt) based impute | ptImpute |
| RUV for phosphoproteomics data normalisation | RUVphospho RUVproteome |
| Site- and condition-specific (sc) impute | scImpute |
| Select by treatment groups (replicate block) | selectGrps |
| Select phosphosites by localisation score | selectLocalisedSites |
| Select phosphosite by percentage of quantification | selectOverallPercent |
| selectTimes | selectTimes |
| PhosR Signalomes | Signalomes |
| Phosphosite annotation | siteAnnotate |
| A list of Stably Phosphorylated Sites (SPSs) | SPSs |
| Standardisation | standardise |
| Tail-based impute | tImpute |
