Entry: error.correction
Aliases: estimate.errors.mean compute.sequence.neighbors em.estimate.error.given
Keywords: error
Description: Estimate sequencing errors and compute corrected counts
URL: ../../../library/sagenhaft/html/error.correction.html

Entry: extract.lib
Aliases: extract.lib.from.zip extract.lib.from.directory extract.library.tags compute.unique.tags combine.libs remove.sage.artifacts read.phd.file read.seq.qual.filepair extract.ditags reestimate.lib.from.tagcounts SAGEartifacts
Keywords: manip
Description: Functions for SAGE library extraction
URL: ../../../library/sagenhaft/html/extract.lib.html

Entry: sage.library
Aliases: read.sage.library write.sage.library plot.sage.library summary.sage.library print.sage.library
Keywords: IO
Description: Class sage.library
URL: ../../../library/sagenhaft/html/sage.library.html

Entry: sage.library.comparison
Aliases: read.sage.library.comparison write.sage.library.comparison plot.sage.library.comparison summary.sage.library.comparison print.sage.library.comparison compare.lib.pair
Keywords: IO
Description: Class sage.library.comparison
URL: ../../../library/sagenhaft/html/sage.library.comparison.html

Entry: sage.test
Aliases: sage.test
Keywords: htest
Description: Compare Two SAGE Libraries
URL: ../../../library/sagenhaft/html/sage.test.html

Entry: sage.utilities
Aliases: tagnum2tagmatrix tagmatrix2tagnum tagnum2tagsequence tagsequence2tagnum revcomp create.matrix.csr table.sparse difference.scatter.plot
Keywords: utilities
Description: Utilities
URL: ../../../library/sagenhaft/html/sage.utilities.html

Entry: sagelibrary.simulate
Aliases: sagelibrary.simulate
Keywords: misc
Description: Simulate SAGE libraries
URL: ../../../library/sagenhaft/html/sagelibrary.simulate.html
