DESCRIPTION

Package: epitopefindr
Type: Package
Title: Minimal Overlaps from BLAST Alignments
Version: 1.1.31
Authors@R: c(person("Brandon", "Sie", role = c("aut", "cre"),
                    email = "brandonsie@gmail.com"),
             person("Ben", "Larman", role = "ctb"),
             person("Daniel", "Monaco", role = "ctb"),
             person("Athena", "Chen", role = "ctb"))
Maintainer: Brandon Sie <brandonsie@gmail.com>
Description: The purpose of this tool is to describe the alignments among a set of peptide sequences by reporting the overlaps of each peptide's alignments to other peptides in the set. One can imagine inputting a list of peptides enriched by immunoprecipitation to identify corresponding epitopes.
License: GPL-3 + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.3
Collate: 
    'epitopefindr.R'
    'addPepSeq.R'
    'chooseIndex.R'
    'cycleBLAST.R'
    'data.R'
    'decipherGaps.R'
    'epfind.R'
    'epPB.R'
    'epitopeBLAST.R'
    'filterBLAST.R'
    'groupMSA.R'
    'indexEpitopes.R'
    'indexGroups.R'
    'isOverlapping.R'
    'makeIR.R'
    'mergeFastaDuplicates.R'
    'numAlignments.R'
    'organizeBLAST.R'
    'outputTable.R'
    'pbCycleBLAST.R'
    'prepareBLAST.R'
    'qsSwap.R'
    'queryBLASTaa.R'
    'removeSmallAln.R'
    'renameBLAST.R'
    'renameFasta.R'
    'selfBLASTaa.R'
    'threshBLAST.R'
    'tidyBLAST.R'
    'tidyFasta.R'
    'trimEpitopes.R'
    'unmergeFastaDuplicates.R'
    'writeFastaAA.R'
    'zzz.R'
Remotes: 
    mhahsler/rBLAST, 
    brandonsie/pdfuniter,
    bioc::3.10/Biostrings, 
    bioc::3.10/IRanges, 
    bioc::3.10/msa, 
    bioc::3.10/S4Vectors
Imports: 
    data.table,
    magrittr,
    seqinr,
    msa,
    stringr,
    tools,
    rBLAST,
    readr,
    microseq,
    IRanges,
    S4Vectors,
    dplyr,
    tidyr,
    Biostrings,
    utils,
    pdfuniter,
    staplr,
    tidytable
Suggests: 
    knitr,
    rmarkdown,
    pdftools,
    igraph,
    foreach,
    doParallel
VignetteBuilder: knitr
Depends: R (>= 3.5)