Man pages for brandonsie/epitopefindr
Minimal Overlaps from BLAST Alignments

addPepSeqAdd/update column in blast table listing peptide names.
chooseIndexIdentifies which of a set of remaining peptides from a blast...
cycleBLASTRepeatedly call epitopeBLAST to iterate through all index...
decipherGapsSplit gapped BLAST alignments into smaller ungapped...
epfindAll-in-one function to call the major steps of epitopefindr.
epitopeBLASTIdentifies next index peptide, calls indexEpitopes to parse...
epitopefindrepitopefindr: a package for identifying minimal overlaps from...
epitopefindrEnv.onload Set stringsAsFactors FALSE for epitopefindr
epPBEpitope progress bar, epPB calls utils::txtProgressBar with...
filterBLASTRemove singletons, sequneces with no non-self alignments,...
groupMSAGenerate pdf multiple sequence alignment logos for identified...
indexEpitopesFor a specified index peptide, identify the maximal intervals...
indexGroupsGroup trimmed sequences into aligning groups
isOverlappingChecks whether the stard/end pos in pattern overlaps with the...
makeIRConverts a two-column data frame to an IRanges object for...
mergeFastaDuplicatesIf two fasta entries have the same sequence, keep only one...
numAlignmentsAdd/update column to blast table listing # of alignments per...
organizeBLASTRename unwieldy columns from rBLAST output table.
outputTableGenerates spreadsheet of reportable data on identified...
pairwise_viral_hitsVirscan hits from AVARDA patient 1
pbCycleBLASTInitialize a txtProgressBar object with which to call...
prepareBLASTCall series of functions to standardize BLAST table for...
qsSwapSwap query and subject data from a BLAST table.
queryBLASTaaBLAST query sequence against a database of sequences.
removeSmallAlnDelete rows in blast table for which the alignment is fewer...
renameBLASTRevert qID and sID columns of blast table back to original...
renameFastaRevert peptide names of a fasta file back to original names...
selfBLASTaaRun BLASTp on amino acid sequences against themselves.
threshBLASTSubset initial BLAST alignbment table to only include...
tidyBLASTCall a series of functions to tidy raw BLAST alignment table...
tidyFastaRemove filler sequences after "." stop codon and cterminal...
trimEpitopesUpdate BLAST table positions to reflect smaller intervals...
unmergeFastaDuplicatesIf a fasta entry has a concatenated name, e.g. from a...
writeFastaAATakes data frame with $Seq and $ID or AAStringSet and writes...
brandonsie/epitopefindr documentation built on June 26, 2020, 10 a.m.