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Bioconductor Changlog.
Fri, 06 Jun 2008
BCRANK
New default values, small change in manual
Biostrings
Fixed small problem with PWMscore(), matchPWM() and countPWM(). Made extractAllMatches() work with a MaskedXString subject (masks are dropped). Added "matchProbePair" method for MaskedDNAString objects. Now use BSgenome.Dmelanogaster.UCSC.dm3 >= 1.3.7 (sequence have masks) instead of BSgenome.Dmelanogaster.FlyBase.r51 in all examples. Other small improvements to several man pages. Reorganized and updated NEWS (moved the file one level up) and TODO files. Bumped version to 2.9.20
A first pass at some simple RUnit tests for pairwiseAlignment.
Minor bug fix in aligned.
Added "reverse" methods for IRanges, NormalIRanges, MaskCollection and MaskedXString objects, and "complement" and "reverseComplement" methods for MaskedDNAString and MaskedRNAString objects.
Add vcountPattern, to count occurrend of pattern in XStringSet-derived
objects