Introduction | Generating a peptideSet | Adding peptide informations | Normalization | Data smoothing | Making calls | Results | shinyApp | Quick analysis | sessionInfo
Package: pepStat 1.47.0
Gregory C Imholte
pepStat: Statistical analysis of peptide microarrays
Statistical analysis of peptide microarrays
Authors:
pepStat_1.47.0.tar.gz
pepStat_1.47.0.zip(r-4.7)pepStat_1.47.0.zip(r-4.6)pepStat_1.47.0.zip(r-4.5)
pepStat_1.47.0.tgz(r-4.6-any)pepStat_1.47.0.tgz(r-4.5-any)
pepStat_1.47.0.tar.gz(r-4.7-any)pepStat_1.47.0.tar.gz(r-4.6-any)
pepStat_1.47.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
pepStat/json (API)
| # Install 'pepStat' in R: |
| install.packages('pepStat', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rglab/pepstat/issues
On BioConductor:pepStat-1.47.0(bioc 3.24)pepStat-1.46.0(bioc 3.23)
Last updated from:2688026c7c. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 251 | ||
| linux-devel-x86_64 | NOTE | 336 | ||
| source / vignettes | OK | 282 | ||
| linux-release-x86_64 | NOTE | 334 | ||
| macos-release-arm64 | NOTE | 136 | ||
| macos-oldrel-arm64 | NOTE | 146 | ||
| windows-devel | NOTE | 220 | ||
| windows-release | NOTE | 193 | ||
| windows-oldrel | NOTE | 225 | ||
| wasm-release | OK | 181 |
Exports:cladecreate_dbfeatureIDmakeCallsmakePeptideSetnormalizeArraypeptidepeptide<-pepZscorepepZscore<-plotArrayImageplotArrayResidualspositionrangesranges<-restabshinyPepStatshowslidingMeansummarizePeptideswidth
Dependencies:BiobaseBiocGenericsclicpp11data.tabledotCall64farverfieldsgenericsGenomicRangesggplot2gluegtableIRangesisobandlabelinglifecyclelimmamapsplyrR6RColorBrewerRcpprlangS4VectorsS7scalesSeqinfospamstatmodvctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Substract baseline intensities | baseline_correct |
| Substract baseline intensities | baselineCorrect.pSet |
| Create a peptide collection | create_db |
| Make antibody binding positivity calls | makeCalls |
| peptideSet constructor | makePeptideSet |
| Normalize tiling array data using sequence information | NormalizeArray normalizeArray |
| peptideSet class | peptideSet peptideSet-class |
| peptideSet methods | clade clade,GRanges-method clade,peptideSet-method clade-methods end,peptideSet-method featureID featureID,peptideSet-method featureID-method peptide peptide,peptideSet-method peptide-method peptide<- peptide<-,peptideSet,character-method peptideSet-methods pepZscore pepZscore,GRanges-method pepZscore,peptideSet-method pepZscore-method pepZscore<- pepZscore<-,GRanges,data.frame-method pepZscore<-,peptideSet,data.frame-method position position,peptideSet-method position-method ranges,peptideSet-method ranges<-,peptideSet-method show,peptideSet-method start,peptideSet-method subset,peptideSet-method summary,peptideSet-method values,peptideSet-method width,peptideSet-method [,peptideSet,ANY,ANY,ANY-method |
| Plot microarray images | plotArrayImage plotArrayResiduals |
| Result table | restab |
| Launch the pepStat Shiny Application | shinyPepStat |
| Data smoothing for peptide microarray. | slidingMean |
| Add information to a peptideSet and summarize peptides | summarizePeptides |