AAAlignment-class       "AAAlignment" result of pairwise sequence
                        alignment.
AAAlphabet-class        Class "AAAlphabet" Amino Acid Alphabet
AASequence              AASequence constructor
AASequence-class        "AASequence" Object representation of a protein
                        Sequence
AASequenceList-class    Class "AASequenceList" - Container
EPAM110                 Amino Acid Substitution matrices
Submatrix-class         Class "Submatrix" Substitution Matrix
computeTm               Computing of melting temperature
crosshyb                Identify probes affected by crosshybridization
crosshyb.out            Output of crosshyb
crosshyb2xls            Write corruptor and corrupted probes to files
crosshyb2xls.putative   Writing list of analyzed probes to file
crosshybDetector-package
                        Detection of cross-hybridization events in
                        microarray experiments
crosshybImage           Spatial distribution of corruptor and corrupted
                        probes
crosshybMAplot          MA-plot
crosshybMCplot          Plot of Monte Carlo simulations
crosshyb_func           Computing cross-hybrization pvalues
extractBadProbes        Extract corruptor and corrupted probes
getSeqs                 Read sequences
list2ascii              Write R list
listdist-methods        Compute distance matrix from a list
probeSeq                Sequence data
raw                     marrayRaw example data
readFasta-methods       reader for databases in Fasta file format.
rg2ma                   Convert intensities to ratios
salign-methods          Optimal pairwise alignment of two protein
                        sequences.
testalign-methods       Scoring of optimal alingments.
