Package: pepitope 0.99.2

Michael Schubert

pepitope: Extract, QC and Screen Peptide Epitopes

Supports T cell receptor neoantigen co-culture screen analysis from peptide library design to sequencing quality control and differential abundance testing. The package annotates somatic variants and RNA fusions, extracts mutant and reference peptide context, prepares barcoded minigene construct tables, counts sample and construct barcodes from sequencing data, and identifies immunogenic epitopes in dropout screens.

Authors:Michael Schubert [aut, cre]

pepitope_0.99.2.tar.gz
pepitope_0.99.2.zip(r-4.7)pepitope_0.99.2.zip(r-4.6)pepitope_0.99.2.zip(r-4.5)
pepitope_0.99.2.tgz(r-4.6-x86_64)pepitope_0.99.2.tgz(r-4.6-arm64)pepitope_0.99.2.tgz(r-4.5-x86_64)pepitope_0.99.2.tgz(r-4.5-arm64)
pepitope_0.99.2.tar.gz(r-4.7-arm64)pepitope_0.99.2.tar.gz(r-4.7-x86_64)pepitope_0.99.2.tar.gz(r-4.6-arm64)pepitope_0.99.2.tar.gz(r-4.6-x86_64)
pepitope_0.99.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
pepitope/json (API)
NEWS

# Install 'pepitope' in R:
install.packages('pepitope', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mschubert/pepitope/issues

Uses libs:
  • zlib– Compression library
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

dnaseqvariantannotationimmunooncologyzlibcpp

4.29 score 4 scripts 31 exports 120 dependencies

Last updated from:0146b1ec6c. Checks:12 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE338
linux-devel-arm64NOTE599
linux-devel-x86_64NOTE634
source / vignettesOK577
linux-release-arm64NOTE565
linux-release-x86_64NOTE611
macos-release-arm64NOTE469
macos-release-x86_64NOTE1033
macos-oldrel-arm64NOTE433
macos-oldrel-x86_64NOTE1047
windows-develNOTE672
windows-releaseNOTE599
windows-oldrelNOTE672
wasm-releaseOK286

Exports:annotate_codingannotate_fusionsassaycolDatacount_fastqexample_barcodesexample_fastqexample_peptidesfilter_fusionsfilter_variantsgenomemake_peptidesmake_reportpep_tileplot_barcode_overlapplot_distrplot_read_countplot_read_distrplot_read_structureplot_readsplot_screenreadVcfAsVRangesremove_cutsiterowDatascreen_calcseqinfoseqlevelsseqlevelsStyleseqlevelsStyle<-subset_contextsubset_context_fusion

Dependencies:abindAnnotationDbiAnnotationFilteraskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcigarilloclicliprcodetoolscpp11crayoncurlDBIDelayedArrayDESeq2dplyrensembldbfarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2ggppggrepelgluegridExtragtablegtoolshmshttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelazyevallifecyclelocfitlubridatemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpatchworkpillarpkgconfigplyrpngpolynomprettyunitsprogressProtGenericspurrrR6RColorBrewerRcppRcppArmadilloRCurlreadrreshape2restfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystringdiststringistringrSummarizedExperimentsystibbletidyrtidyselecttimechangetzdbUCSC.utilsutf8VariantAnnotationvctrsviridisLitevroomwithrXMLxtsXVectoryamlzoo

Co-culture screen

Rendered fromscreen.Rmdusingknitr::rmarkdownon Jun 18 2026.

Last update: 2026-06-18
Started: 2025-03-06

Minigene report

Rendered fromminigene.Rmdusingknitr::rmarkdownon Jun 18 2026.

Last update: 2025-08-02
Started: 2025-08-02

Quality control

Rendered fromqc.Rmdusingknitr::rmarkdownon Jun 18 2026.

Last update: 2026-06-18
Started: 2025-03-06