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| combine.libs | Functions for SAGE library extraction |
| compare.lib.pair | Class sage.library.comparison |
| compute.sequence.neighbors | Estimate sequencing errors and compute corrected counts |
| compute.unique.tags | Functions for SAGE library extraction |
| create.matrix.csr | Utilities |
| difference.scatter.plot | Utilities |
| em.estimate.error.given | Estimate sequencing errors and compute corrected counts |
| estimate.errors.mean | Estimate sequencing errors and compute corrected counts |
| extract.ditags | Functions for SAGE library extraction |
| extract.lib.from.directory | Functions for SAGE library extraction |
| extract.lib.from.zip | Functions for SAGE library extraction |
| extract.library.tags | Functions for SAGE library extraction |
| plot.sage.library | Class sage.library |
| plot.sage.library.comparison | Class sage.library.comparison |
| print.sage.library | Class sage.library |
| print.sage.library.comparison | Class sage.library.comparison |
| read.phd.file | Functions for SAGE library extraction |
| read.sage.library | Class sage.library |
| read.sage.library.comparison | Class sage.library.comparison |
| read.seq.qual.filepair | Functions for SAGE library extraction |
| reestimate.lib.from.tagcounts | Functions for SAGE library extraction |
| remove.sage.artifacts | Functions for SAGE library extraction |
| revcomp | Utilities |
| sage.test | Compare Two SAGE Libraries |
| SAGEartifacts | Functions for SAGE library extraction |
| sagelibrary.simulate | Simulate SAGE libraries |
| summary.sage.library | Class sage.library |
| summary.sage.library.comparison | Class sage.library.comparison |
| table.sparse | Utilities |
| tagmatrix2tagnum | Utilities |
| tagnum2tagmatrix | Utilities |
| tagnum2tagsequence | Utilities |
| tagsequence2tagnum | Utilities |
| write.sage.library | Class sage.library |
| write.sage.library.comparison | Class sage.library.comparison |