Package: pepStat 1.41.0
Gregory C Imholte
pepStat: Statistical analysis of peptide microarrays
Statistical analysis of peptide microarrays
Authors:
pepStat_1.41.0.tar.gz
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pepStat_1.41.0.tgz(r-4.4-any)pepStat_1.41.0.tgz(r-4.3-any)
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pepStat.pdf |pepStat.html✨
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-1.39.0(bioc 3.20)pepStat-1.38.0(bioc 3.19)
Last updated 22 days agofrom:42e8f77117. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | NOTE | Oct 31 2024 |
| R-4.5-linux | NOTE | Oct 30 2024 |
| R-4.4-win | NOTE | Oct 31 2024 |
| R-4.4-mac | NOTE | Oct 31 2024 |
| R-4.3-win | NOTE | Oct 31 2024 |
| R-4.3-mac | NOTE | Oct 31 2024 |
Exports:cladecreate_dbfeatureIDmakeCallsmakePeptideSetnormalizeArraypeptidepeptide<-pepZscorepepZscore<-plotArrayImageplotArrayResidualspositionrangesranges<-restabshinyPepStatshowslidingMeansummarizePeptideswidth
Dependencies:askpassBiobaseBiocGenericsclicolorspacecurldata.tabledotCall64fansifarverfieldsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglatticelifecyclelimmamagrittrmapsMASSMatrixmgcvmimemunsellnlmeopensslpillarpkgconfigplyrR6RColorBrewerRcpprlangS4VectorsscalesspamstatmodsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc
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 |