annotateAHO             annotate peptides using AhoCorasickTrie
annotatePeptides        Annotate peptides with protein ids
annotateVec             annotate vector of petpide sequences against
                        fasta file (Deprecated)
createDecoyDB           create db with decoys and contaminants
filterSequences         Filter for specific residues
greedy                  given matrix (columns protein rows peptides),
                        compute minimal protein set using greedy
                        algorithm
greedyRes2Matrix        converts result of greedy function to a matrix
                        with 3 columns - peptide - charge and protein
loadContaminantsFasta   load list of contaminant sequences
loadContaminantsNoHumanFasta
                        load list of contaminant without human
                        sequences
loadHomoSapiensSignalPeptides
                        load human signal peptides
loadMusMusculusSignalPeptides
                        load mus musculus signal peptides
makeID                  make id for chain in format
                        sp|P30443|1A01_HUMANs25
makeIDUnip              make id for chain compatible with uniprot
pepprot                 Table containing peptide information
prepareMatrix           given table of peptide protein assigments
                        generate matrix
protpepmeta             Generated from pepprot using method
                        annotatePeptides
protpepmetashort        Small version of pepprot dataset to speed up
                        computation
prozor                  Minimal Protein set Explaining Peptides
readPeptideFasta        wrapper setting the correct parameters
removeSignalPeptide     remove signal peptides from main chain
reverseSeq              create rev sequences to fasta list
writeFasta              write fasta lists into file
