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Bioconductor Changlog.
Tue, 20 May 2008
GGtools
various doc improvements to pass check cleanly on 2.8
pass on windows
ok
passing check on gladstone
GGBase
bad table name in man removed
fix table name
needed to update the sqlite for annotation to include offsets and version 23a contents
gaga
Deleted unnecessary files
Deleted unnecessary files
Submitted version 1.0.0
limma
20 May 2008: limma 2.15.4
- Cleaning up of source code in find_saddle_theta2.c and
corresponding calls in background-normexp-mle.R. No user
visible changes. The C code now passes R CMD check without
warnings, and superfluous utility functions are removed from
background-normexp-mle.R
ShortRead
bug fixes plus more solexa export qa reporting
alphabetScore, to calculate sum of scores across nucleotides in a read
qa revisions
- SolexaExport for parsing export files
- some interface work, but more to come
internal changes
- 'decoder' to select appropriate decode function
quality
- no warnings abuout ignoring baseOnly for quality of Fastq-derived objects
gcrma
I have fixed a bug in the base.profiles2.R function where a parentheses was misplaced.
CoCiteStats
this is going to break until the paperLen issue is resolved, but at least
humanLLMappings is gone, for now
this is going to break
plw
Bumped Z
xps
correct compile error
spkTools
Updated documentation