Bioconductor Changelog
   


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ABarray
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EBImage
EBarrays
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GGBase
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buildBioC
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codelink
codetoolsBioC
convert
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cosmo
cosmoGUI
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daMA
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ecolitk
edd
edgeR
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graph
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iterativeBMA
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lapmix
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logitT
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maanova
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ontoTools
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reb
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rflowcyt
rhdf5
rnaSeqTests
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rtracklayer
safe
sagenhaft
seqLogo
sigPathway
siggenes
simpleaffy
simulatorAPMS
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smoothMiner
snapCGH
snpMatrix
spikeLI
spkTools
splicegear
splots
spotSegmentation
sscore
ssize
stam
stepNorm
syslibGTK
tilingArray
timecourse
tkWidgets
topGO
tspair
twilight
vbmp
vsn
weaver
webbioc
widgetInvoke
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xcms
xcmsGUI
xmapbridge
xps
yaqcaffy


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Tue, 13 Oct 2009

EBImage
fixed R CMD check memory leak (caused by a ReadImage() call after a drawtext() one); this was due to the MagickWandTerminus() destructor which also destroy MagickCore services (! see on ImageMagick wand/magick-wand.c for details)

[/EBImage] permanent link

metahdep
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.

[/metahdep] permanent link

Rintact
updated the list2matrix function and man page

[/Rintact] permanent link

chipseq
Deprecate most of the context functions (moved to
GenomicFeatures). The context distribution stuff is ported, but untested.

[/chipseq] permanent link

bgx
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.

[/bgx] permanent link

yaqcaffy
yaqc.summary manual update
added summary(YAQCStatsObject) function

[/yaqcaffy] permanent link

AnnotationDbi
adding to the TODO list

[/AnnotationDbi] permanent link

AnnotationDbi
Adds parameter for the inpIDMapper function.
This just adds another parameter so that you can choose to have the
final results limited to only one answer per initial ID even if you
map to something like a uniprot which may have many IDs for each
entrez gene ID. Default will still give you all of whatever you asked
for.
Added convenience function inpIDMapper
This function allows for easy mapping (using the appropriate
inparanoid packages) for IDs between species.

[/AnnotationDbi] permanent link

SemSim
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.

[/SemSim] permanent link

chipseq
some cleanup
changed interpretation of nsteps

[/chipseq] permanent link

LMGene
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.

[/LMGene] permanent link

chipseq
Another simulateReads rev.
Further speedup to simulateReads.
Further improvements to simulateReads function.
Improved performance of simulateReads.
Changed simulateReads function to use ShortReadQ class output

[/chipseq] permanent link

AnnotationDbi
This consolidates the INPARANOID_DB schemas into one.
By consolodating the INPARANOID schemas into one INPARANOID_DB schema,
I can now add more inparanoid packages without bloating up
AnnotationDbi any more than is strictly necessary...

[/AnnotationDbi] permanent link

chipseq
added alpha.hat to list of things computed

[/chipseq] permanent link

pdInfoBuilder
Prep'ing to add 2nd version of db-based annotation

[/pdInfoBuilder] permanent link

AnnotationDbi
end of testing.
testing

[/AnnotationDbi] permanent link

SPIA
small bug fix and vignette update

[/SPIA] permanent link

chipseq
Adjusted the number of bins in the density calculations.

[/chipseq] permanent link

AnnotationDbi
Fixes a small bug in SQLForge and expands inpIDMapper.
This fixes a small bug where SQLForge fails when organsisms don't have
unigene IDs, and also expands the number of species that inpIDMapper
should work for.

[/AnnotationDbi] permanent link

pdInfoBuilder
Fixed merging of POS and NDF files

[/pdInfoBuilder] permanent link

chipseq
one more mod
typo
one more set of tweaks
last piece
more updates to get the simulation code working

[/chipseq] permanent link

SPIA
updated pathway data by including interactions between genes and KEGG groups that contain at least one gene

[/SPIA] permanent link

AnnotationDbi
This adds support for worm, pig and chicken.
Adds code for planned support (October release) of these additional
organisms. These organisms are not supported at this moment.

[/AnnotationDbi] permanent link

RLMM
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.

[/RLMM] permanent link

EBImage
New EBImage.dll compiled with R2.7.0, GTK 2.12.9 and ImageMagick 6.4.1

[/EBImage] permanent link

AnnotationDbi
Adds convenience function for listing .db0 packages.

[/AnnotationDbi] permanent link

AnnotationDbi
Major overhaul for chip packages.
This checkin includes changes to allow chip packages to be lightweight
and instead depend on organism packages for their data. It also adds
organism support for rhesus monkeys, chimpanzees, Anopheles mosquito,
Arabidopsis and Xenopus laevis.

[/AnnotationDbi] permanent link

codetoolsBioC
Made error message more informative.
Stopped using ":::" operator since it doesn't support extraction from packages without namespaces.
Used Luke's suggestion to pass a modified collectUsageLeaf function into makeUsageCollector so the findGlobals search enters closures.
Recreate functions from scratch before passing to findGlobals function.

[/codetoolsBioC] permanent link

EBImage
Tried to provide a slightly more instructive warning when GTK+ cannot
be initialised at run-time.

[/EBImage] permanent link

GraphAT
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.

[/GraphAT] permanent link

maanova
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.

[/maanova] permanent link

CGHbase
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.

[/CGHbase] permanent link

SPIA
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.

[/SPIA] permanent link

Rintact
Fixed Rintact dependencies so package will pass check.

[/Rintact] permanent link

macat
fixes for enabling HTML output with .db data packages

[/macat] permanent link

macat
Replaced usage of soon to be defunct class exprSet with ExpressionSet.

[/macat] permanent link

BicARE
This add BicARE, arrayMvout and affyContam to bioconductor.

[/BicARE] permanent link

cosmo
Fixed small bug in reverse complement calculation pointed out by Heejung

[/cosmo] permanent link

macat
fix to handle .db annotation packages

[/macat] permanent link

pdInfoBuilder
Cleaning up package, exporting only used classes
Added TilingFeatureSet2 class to handle 2-colors applications of tiling arrays. Redefined the FeatureSet class and sampleNames method. Removed unused class.

[/pdInfoBuilder] permanent link