| addPepSeq | Add/update column in blast table listing peptide names. |
| chooseIndex | Identifies which of a set of remaining peptides from a blast... |
| cycleBLAST | Repeatedly call epitopeBLAST to iterate through all index... |
| decipherGaps | Split gapped BLAST alignments into smaller ungapped... |
| epfind | All-in-one function to call the major steps of epitopefindr. |
| epitopeBLAST | Identifies next index peptide, calls indexEpitopes to parse... |
| epitopefindr | epitopefindr: a package for identifying minimal overlaps from... |
| epitopefindrEnv | .onload Set stringsAsFactors FALSE for epitopefindr |
| epPB | Epitope progress bar, epPB calls utils::txtProgressBar with... |
| filterBLAST | Remove singletons, sequneces with no non-self alignments,... |
| groupMSA | Generate pdf multiple sequence alignment logos for identified... |
| indexEpitopes | For a specified index peptide, identify the maximal intervals... |
| indexGroups | Group trimmed sequences into aligning groups |
| isOverlapping | Checks whether the stard/end pos in pattern overlaps with the... |
| makeIR | Converts a two-column data frame to an IRanges object for... |
| mergeFastaDuplicates | If two fasta entries have the same sequence, keep only one... |
| numAlignments | Add/update column to blast table listing # of alignments per... |
| organizeBLAST | Rename unwieldy columns from rBLAST output table. |
| outputTable | Generates tables of reportable data on identified minimal... |
| pairwise_viral_hits | Virscan hits from AVARDA patient 1 |
| pbCycleBLAST | Initialize a txtProgressBar object with which to call... |
| prepareBLAST | Call series of functions to standardize BLAST table for... |
| qsSwap | Swap query and subject data from a BLAST table. |
| queryBLASTaa | BLAST query sequence against a database of sequences. |
| removeSmallAln | Delete rows in blast table for which the alignment is fewer... |
| renameBLAST | Revert qID and sID columns of blast table back to original... |
| renameFasta | Revert peptide names of a fasta file back to original names... |
| selfBLASTaa | Run BLASTp on amino acid sequences against themselves. |
| threshBLAST | Subset initial BLAST alignbment table to only include... |
| tidyBLAST | Call a series of functions to tidy raw BLAST alignment table... |
| tidyFasta | Remove filler sequences after "." stop codon and cterminal... |
| trimEpitopes | Update BLAST table positions to reflect smaller intervals... |
| unmergeFastaDuplicates | If a fasta entry has a concatenated name, e.g. from a... |
| writeFastaAA | Takes data frame with $Seq and $ID or AAStringSet and writes... |
