Files in brandonsie/epitopefindr
Minimal Overlaps from BLAST Alignments

.Rbuildignore
.gitattributes
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md R/addPepSeq.R R/chooseIndex.R R/cycleBLAST.R R/data.R R/decipherGaps.R R/epPB.R R/epfind.R R/epitopeBLAST.R R/epitopefindr.R R/filterBLAST.R R/groupMSA.R R/indexEpitopes.R R/indexGroups.R R/isOverlapping.R R/makeIR.R R/mergeFastaDuplicates.R R/numAlignments.R R/organizeBLAST.R R/outputTable.R R/pbCycleBLAST.R R/prepareBLAST.R R/qsSwap.R R/queryBLASTaa.R R/removeSmallAln.R R/renameBLAST.R R/renameFasta.R R/selfBLASTaa.R R/threshBLAST.R R/tidyBLAST.R R/tidyFasta.R R/trimEpitopes.R R/unmergeFastaDuplicates.R R/writeFastaAA.R R/zzz.R TODO.md
_config.yml
_pkgdown.yml
data/pairwise_viral_hits.rda
docs/404.html
docs/LICENSE-text.html
docs/TODO.html
docs/apple-touch-icon-120x120.png
docs/apple-touch-icon-152x152.png
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docs/apple-touch-icon.png
docs/articles/epitopefidnr_avarda_vignette.html
docs/articles/epitopefidnr_avarda_vignette_files/figure-html/igraph-1.png
docs/articles/epitopefindr_avarda_vignette.html
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docs/articles/index.html
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docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/readme.html
docs/reference/addPepSeq.html
docs/reference/chooseIndex.html
docs/reference/cycleBLAST.html
docs/reference/dbCleanup.html
docs/reference/decipherGaps.html
docs/reference/epFind2.html
docs/reference/epPB.html
docs/reference/epSetupBLAST.html
docs/reference/epSetupDirectory.html
docs/reference/epSetupPeptides.html
docs/reference/epfind.html
docs/reference/epitopeBLAST.html
docs/reference/epitopefindr.html
docs/reference/epitopefindrEnv.html
docs/reference/filterBLAST.html
docs/reference/glAssign.html
docs/reference/glGet.html
docs/reference/glParamAssign.html
docs/reference/glParamGet.html
docs/reference/groupMSA.html
docs/reference/index.html
docs/reference/indexEpitopes.html
docs/reference/indexGroups.html
docs/reference/isOverlapping.html
docs/reference/makeIR.html
docs/reference/mergeFastaDuplicates.html
docs/reference/numAlignments.html
docs/reference/organizeBLAST.html
docs/reference/outputFiles.html
docs/reference/outputTable.html
docs/reference/pairwise_viral_hits.html
docs/reference/pbCycleBLAST.html
docs/reference/prepareBLAST.html
docs/reference/printSignpost.html
docs/reference/qsSwap.html
docs/reference/queryBLASTaa.html
docs/reference/removeSmallAln.html
docs/reference/renameBLAST.html
docs/reference/renameFasta.html
docs/reference/selfBLASTaa.html
docs/reference/threshBLAST.html
docs/reference/tidyBLAST.html
docs/reference/tidyFasta.html
docs/reference/trimEpitopes.html
docs/reference/unmergeFastaDuplicates.html
docs/reference/writeFastaAA.html
docs/sitemap.xml
logo.svg
man/addPepSeq.Rd man/chooseIndex.Rd man/cycleBLAST.Rd man/decipherGaps.Rd man/epPB.Rd man/epfind.Rd man/epitopeBLAST.Rd man/epitopefindr.Rd man/epitopefindrEnv.Rd man/filterBLAST.Rd man/groupMSA.Rd man/indexEpitopes.Rd man/indexGroups.Rd man/isOverlapping.Rd man/makeIR.Rd man/mergeFastaDuplicates.Rd man/numAlignments.Rd man/organizeBLAST.Rd man/outputTable.Rd man/pairwise_viral_hits.Rd man/pbCycleBLAST.Rd man/prepareBLAST.Rd man/qsSwap.Rd man/queryBLASTaa.Rd man/removeSmallAln.Rd man/renameBLAST.Rd man/renameFasta.Rd man/selfBLASTaa.Rd man/threshBLAST.Rd man/tidyBLAST.Rd man/tidyFasta.Rd man/trimEpitopes.Rd man/unmergeFastaDuplicates.Rd man/writeFastaAA.Rd
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
readme.md
vignettes/.gitignore
vignettes/AVARDA_vignette_data/epitopeKey.csv
vignettes/AVARDA_vignette_data/epitopeSummary.csv
vignettes/AVARDA_vignette_data/finalAlignments.csv
vignettes/AVARDA_vignette_data/msa.pdf
vignettes/AVARDA_vignette_data/png/msa-11.png
vignettes/epitopefindr_avarda_vignette.Rmd
brandonsie/epitopefindr documentation built on June 26, 2020, 10 a.m.