Man pages for brandonsie/epitopefindr
Minimal Overlaps from BLAST Alignments

addPepSeqaddPepSeq Add/update column in blast table listing peptide...
chooseIndexIdentifies which of a set of remaining peptides from a blast...
cycleBLASTcycleBLAST Repeatedly call epitopeBLAST to iterate through...
dbCleanupdbCleanup Directory management for epitopefindr
decipherGapsdecipherGaps Split gapped BLAST alignments into smaller...
epFindepFind All-in-one function to call the major steps of...
epitopeBLASTepitopeBLAST Identifies next index peptide, calls...
epitopefindrepitopefindr: a package for identifying minimal overlaps from...
epitopefindrEnv.onload Set stringsAsFactors FALSE for epitopefindr
epPBepPB, short of epitope progress bar, calls...
epSetupBLASTepSetupBLAST Run BLASTp on input peptides against each other...
epSetupDirectoryepSetupDirectory Setup epitopefinder directory paths
epSetupPeptidesepSetupPeptides Tidy input peptide sequences.
filterBLASTfilterBLAST Remove singletons, sequneces with no non-self...
glAssignglAssign Quick wrapper function for assigning data to global...
glGetglGet Retrieve data from global environment, e.g. from...
glParamAssignglParamAssign Special case of glAssign to update a parameter...
glParamGetglParamGet Special case of glGet to retrieve a value from...
groupMSAgroupMSA Generate pdf multiple sequence alignment logos for...
indexEpitopesindexEpitopes For a specified index peptide, identify the...
indexGroupsindexGroups Group trimmed sequences into aligning groups
isOverlappingisOverlapping Checks whether the stard/end pos in pattern...
makeIRmakeIR converts a two-column data frame to an IRanges object...
mergeFastaDuplicatesmergeFastaDuplicates If two fasta entries have the same...
numAlignmentsnumAlignments Add/update column to blast table listing # of...
organizeBLASTorganizeBLAST Rename unwieldy columns from rBLAST output...
outputFilesoutputFiles Generates some output files to report from the...
outputTableoutputTable Generates spreadsheet of reportable data on...
pbCycleBLASTpbCycleBLAST Initialize a txtProgressBar object with which to...
prepareBLASTprepareBLAST Call series of functions to standardize BLAST...
printSignpostprintSignpost Some status updates that can be printed if...
qsSwapqsSwap Swap query and subject data from a BLAST table.
queryBLASTaaqueryBLASTaa BLAST query sequence against a database of...
removeSmallAlnremoveSmallAln Delete rows in blast table for which the...
selfBLASTaaselfBLASTaa Run BLASTp on amino acid sequences against...
threshBLASTthreshBLAST Subset initial BLAST alignbment table to only...
tidyBLASTtidyBLAST Call a series of functions to tidy raw BLAST...
tidyFastatidyFasta remove filler sequences after "." stop codon and...
trimEpitopestrimEpitopes Update BLAST table positions to reflect smaller...
unmergeFastaDuplicatesunmergeFastaDuplicates
writeFastaAAwriteFastaAA Takes data frame with $Seq and $ID or...
brandonsie/epitopefindr documentation built on Jan. 21, 2019, 3:43 a.m.