Files in brandonsie/epitopefindr

Minimal Overlaps from BLAST Alignments

.Rbuildignore

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.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

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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

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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

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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

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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 Oct. 31, 2021, 5:20 p.m.