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Bioconductor Changlog.
Mon, 20 Apr 2009
oneChannelGUI
fixing bug in RP exon filtering
fixing bug for RP exon filtering
[/oneChannelGUI] permanent link
Sat, 18 Apr 2009
pamr
Back porting change to get package to pass R CMD check.
Rgraphviz
Backporting a low level change to get it to build with newer versions of graphviz.
explorase
Removing support for explorase on pitt.
xps
update to xps-1.2.10
- correct bug in TUnivariateTest::FDR and Hochberg
- add method TUnivariateTest::BY
- update method.UniFilter.R and uniTest-methods.Rd
oneChannelGUI
fix little bugs in exon analysis
[/oneChannelGUI] permanent link
Wed, 08 Apr 2009
MEDME
updated MEDME.R function according to the modification in the drc library
xps
update to xps-1.2.9
- make function exonLevel public and add exonLevel.Rd
- update DESCRIPTION
Biostrings
Trying to have inst/include/_Biostrings_stubs.c understood by Sun Studio 12 C compiler. Bumped version to 2.10.22
IRanges
Trying to have inst/include/_IRanges_stubs.c understood by Sun Studio 12 C compiler. Bumped version to 1.0.16
IRanges
Back porting the _sort_int_array() fix for SunWPro-12 compilers. Version bumped to 1.0.15
xps
update to xps-1.2.8
- upload correct DESCRIPTION
update to xps-1.2.7
- add function MetaProbesets to xps.def
- update rwrapper.cxx
- update script4xps.R, script4exon.R
flowCore
the norm2Filter is now optional when computing the spillover matrix
HilbertVisGUI
added note that mac version is broken
[/HilbertVisGUI] permanent link
Fri, 20 Mar 2009
limma
biocViews entry of Statistics changed to Bioinformatics
20 March 2009: limma 2.16.5
- Bug fix to rowname assignment for MAList and RGList objects
containing matrices in 'other' component
- lmFit() warning message on NA coefficients is now more
refined. It now appears only when the coef vector is
partially NA for some probes.
- Fix to gls.series() so that it does not fail when the
weight matrix contains NA values.
- update to backgroundCorrect help page to reflect published
papers.
- update to treat help page to reflect published paper.
- lmFit now looks for a design matrix in an MAList data object,
if one exists.
- C code dynamic library is loaded when package is loaded
rather than when it is attached, to enable other packages
to import limma. (Not user visible.)
- minor edits to geneSetTest, roast and 08Tests help files.
ShortRead
Fixed a bug in polynFilter when just one nucleotide is selected.
biocViews
Make Rnw file extension case insensitive when managing vignettes.
Made the Rd file extension case insensitive in the pdf reference manual construction function.
BSgenome
Latest changes in Biostrings make runAnalysis2() work again (GenomeSearching.Rnw vignette). Bumped version to 1.10.5
Biostrings
[backport from trunk] More cleaning of the ByPos_MIndex/ByName_MIndex
mess (see comment for commit r37887 in trunk for the details).
Bumped version to 2.10.21
Biostrings
Added DNA_BASES and RNA_BASES constants.
Fixing breakage introduced at r37724 (backport from trunk was incomplete).
Biostrings
Completing the set of methods for matchPattern(), countPattern(), vmatchPattern(), vcountPattern(), matchPDict(), countPDict(), vmatchPDict() and vcountPDict() so that the 4 basic string containers (XString, XStringSet, XStringViews and MaskedXString) are covered. Some of them are just stubs redirecting the user to the appropriate function. Bumped version to 2.10.19
Biostrings
[backport from trunk] Some adjustments to list-like classes MIndex and XStringSet. Made PDict a list-like class too. Bumped version to 2.10.18
IRanges
Backporting the ListLike class and methods from trunk. Bumped version to 1.0.13
biocViews
Adding reference manuals to man pages.
Switched to using vignette index entries in package home pages.
oneChannelGUI
minor updates
[/oneChannelGUI] permanent link
Biostrings
Don't use the ByName_MIndex class anymore (will be removed soon). MIndex objects returned by matchPDict() (and family) are now always of subtype ByPos_MIndex (used to be ByName_MIndex if the 'pdict' arg had names). Bumped version to 2.10.17
edgeR
fixed bug in topTags -- A was calculated incorrectly
biocViews
Back porting recent improvements from BioC 2.4 code line.
edgeR
fixed bug w.r.t. ordering of groups
biocViews
Fixed a typo.
Added an infrastructure to control the body background color of the stylesheet.
xps
update to xps-1.2.6
- update XPSSchemes.cxx to support using genome arrays as exon arrays
- update manual files import.xxx.scheme.Rd
HilbertVisGUI
swapped order in PKG_CONFIG_PATH to avoid build problems on Mac due to old GTK+ installation
[/HilbertVisGUI] permanent link
Sat, 21 Feb 2009
IRanges
Back porting a few bug fixes to the IRanges functionality.
Category
Fix that affects a corner case for KEGGHyperGParams
This fixes a bug that would prevent hyperGTest() from performing as
expected when the annotation package is a chip package.
flowCore
fixed compensation method to be compliant to the standard
Biostrings
Fixed serious bug in vcountPDict(): except for the 1st column of the returned matrix (where all match counts seem to have been correctly reported), in all other columns the match count for any duplicated pattern was always reported to be 0. Bumped version to 2.10.16
gaggle
fixed bug with matrix naming before broadcast
Biostrings
Fixed serious bug in vcountPDict(): except for the 1st column of the returned matrix (where all match counts seem to have been correctly reported), in all other columns the match count for any duplicated pattern was always reported to be 0. Bumped version to 2.10.16
GenomeGraphs
Fix in GenericArray drawing
[/GenomeGraphs] permanent link
Wed, 11 Feb 2009
AnnotationDbi
Added 'drop.invalid.keys' arg to "subset" methods for Bimap and AnnDbBimap
objects (default is FALSE). Bumped version to 1.4.3
[/AnnotationDbi] permanent link