Package: PhIPData 1.15.0
Athena Chen
PhIPData: Container for PhIP-Seq Experiments
PhIPData defines an S4 class for phage-immunoprecipitation sequencing (PhIP-seq) experiments. Buliding upon the RangedSummarizedExperiment class, PhIPData enables users to coordinate metadata with experimental data in analyses. Additionally, PhIPData provides specialized methods to subset and identify beads-only samples, subset objects using virus aliases, and use existing peptide libraries to populate object parameters.
Authors:
PhIPData_1.15.0.tar.gz
PhIPData_1.15.0.zip(r-4.5)PhIPData_1.15.0.zip(r-4.4)PhIPData_1.15.0.zip(r-4.3)
PhIPData_1.15.0.tgz(r-4.4-any)PhIPData_1.15.0.tgz(r-4.3-any)
PhIPData_1.15.0.tar.gz(r-4.5-noble)PhIPData_1.15.0.tar.gz(r-4.4-noble)
PhIPData_1.15.0.tgz(r-4.4-emscripten)PhIPData_1.15.0.tgz(r-4.3-emscripten)
PhIPData.pdf |PhIPData.html✨
PhIPData/json (API)
NEWS
| # Install 'PhIPData' in R: |
| install.packages('PhIPData', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/athchen/phipdata/issues
On BioConductor:PhIPData-1.15.0(bioc 3.21)PhIPData-1.14.0(bioc 3.20)
infrastructuredatarepresentationsequencingcoverage
Last updated 2 months agofrom:3dd94547ef. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 30 2024 |
| R-4.5-win | NOTE | Nov 30 2024 |
| R-4.5-linux | NOTE | Nov 30 2024 |
| R-4.4-win | NOTE | Nov 30 2024 |
| R-4.4-mac | NOTE | Nov 30 2024 |
| R-4.3-win | OK | Nov 30 2024 |
| R-4.3-mac | OK | Nov 30 2024 |
Exports:assay<-assays<-countscounts<-deleteAliasgetAliasgetBeadsNamegetLibrarylibrarySizelistLibrarylogfclogfc<-makeLibrarypeptideInfopeptideInfo<-PhIPDataprobprob<-propReadsremoveLibrarysampleInfosampleInfo<-setAliassetBeadsNamesubsetBeads
Dependencies:abindaskpassBiobaseBiocFileCacheBiocGenericsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrDelayedArraydplyredgeRfansifastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrIRangesjsonlitelatticelifecyclelimmalocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplogrpurrrR6rlangRSQLiteS4ArraysS4VectorsSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Using aliases to subset virus data | aliases deleteAlias getAlias setAlias |
| Defining how beads-only samples are encoded. | defineBeads getBeadsName setBeadsName |
| Calculate total read counts for each sample. | librarySize |
| Peptide libraries | getLibrary listLibrary makeLibrary peptideLibraries removeLibrary |
| The PhIPData class | .PhIPData PhIPData PhIPData-class |
| Accessing and Modifying Information in PhIPData objects | assay<-,PhIPData,character-method assay<-,PhIPData,missing-method assay<-,PhIPData,numeric-method assays<-,PhIPData,list-method assays<-,PhIPData,SimpleList-method counts,PhIPData-method counts<-,PhIPData-method logfc logfc,PhIPData-method logfc<- logfc<-,PhIPData-method peptideInfo peptideInfo,PhIPData-method peptideInfo<- peptideInfo<-,PhIPData-method PhIPData-methods prob prob,PhIPData-method prob<- prob<-,PhIPData-method sampleInfo sampleInfo,PhIPData-method sampleInfo<- sampleInfo<-,PhIPData-method |
| Proportion of sample reads | propReads |
| Subset beads-only samples | subsetBeads |
