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| crosshybDetector-package | Detection of cross-hybridization events in microarray experiments |
| 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 |
| 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 | 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 |
| EBLOSUM50 | Amino Acid Substitution matrices |
| EBLOSUM62 | Amino Acid Substitution matrices |
| EPAM110 | Amino Acid Substitution matrices |
| extractBadProbes | Extract corruptor and corrupted probes |
| frequency-method | "AASequence" Object representation of a protein Sequence |
| getSeqs | Read sequences |
| infogrep | reader for databases in Fasta file format. |
| initialize-method | "AASequence" Object representation of a protein Sequence |
| levels-method | Class "AAAlphabet" Amino Acid Alphabet |
| list2ascii | Write R list |
| listdist | Compute distance matrix from a list |
| listdist-method | Compute distance matrix from a list |
| listdist-methods | Compute distance matrix from a list |
| probeSeq | Sequence data |
| raw | marrayRaw example data |
| readFasta | reader for databases in Fasta file format. |
| readFasta-method | reader for databases in Fasta file format. |
| readFasta-methods | reader for databases in Fasta file format. |
| rg2ma | Convert intensities to ratios |
| salign | Optimal pairwise alignment of two protein sequences. |
| salign-method | Optimal pairwise alignment of two protein sequences. |
| salign-methods | Optimal pairwise alignment of two protein sequences. |
| selfalign | "AASequence" Object representation of a protein Sequence |
| selfalign-method | "AASequence" Object representation of a protein Sequence |
| seqgrep | reader for databases in Fasta file format. |
| show-method | "AAAlignment" result of pairwise sequence alignment. |
| show-method | Class "AAAlphabet" Amino Acid Alphabet |
| show-method | "AASequence" Object representation of a protein Sequence |
| show-method | Class "AASequenceList" - Container |
| show-method | Class "Submatrix" Substitution Matrix |
| subFromEmboss | Class "Submatrix" Substitution Matrix |
| subFromEmboss-method | Class "Submatrix" Substitution Matrix |
| Submatrix | Class "Submatrix" Substitution Matrix |
| Submatrix-class | Class "Submatrix" Substitution Matrix |
| summary-method | "AAAlignment" result of pairwise sequence alignment. |
| testalign | Scoring of optimal alingments. |
| testalign-method | Scoring of optimal alingments. |
| testalign-methods | Scoring of optimal alingments. |
| [-method | Class "AASequenceList" - Container |
| [<--method | Class "AASequenceList" - Container |
| [[<--method | Class "AASequenceList" - Container |