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 |