About
Click here
to learn more about this blog.
Packages
Click on a link
for updates to that package only.
Subscribe
Subscribe to the
Bioconductor Changlog.
Thu, 08 May 2008
flowViz
lpolygon methods now return the gate outlines and the contour function is fixed
flowCore
added parameters method for filterResults
Changed the introduction a little and added a few sentences about plateCore.
Biostrings
Added the read.rmMask() and read.trfMask() functions for reading a mask from a RepeatMasker .out file or from a Tandem Repeats Finder .bed file. No version bump yet.
Added score profiles to pairwiseAligment results to allow users to see how well strings align at different points.
Rintact
i have added the man page
i have added a new method to the package
annotate
Changed useHomology vignette so it won't interfere with build. Will replace with a new version soon.
Biostrings
Added the maskMotif() generic function for masking a sequence by content.
As a consequence, previous 'masks(x) <- "motif"' syntax must be replaced by
new 'x <- maskMotif(x, "motif")' syntax.
Bumped version to 2.9.3
vsn
I added a section to the vignette about the relationship between vsn
parameters and the additive-multiplicative error model.
ontoTools
ok
xcmsGUI
This just creates an empty project for xcmsGUI
arrayQualityMetrics
Correcting the legend when using grouprep =TRUE
[/arrayQualityMetrics] permanent link
Tue, 06 May 2008
oligoClasses
Bug fix: initialize for SnpCopyNumberSet
[/oligoClasses] permanent link
flowCore
small work on the text and add references
Biostrings
Added the coverage() generic function with methods for IRanges, MaskCollection, XStringViews, MaskedXString and MIndex objects. Version bumped to 2.9.2
Changed the algorithm in pairwiseAlignment to start at the end of the strings rather than the beginning to make it easier to get the scores based on alignment starts.
First pass as reworking the pairwiseAlignment infrastructure to use less memory. It is also marginally faster as well.
BiocCaseStudies
cleaned up Description
[/BiocCaseStudies] permanent link
Mon, 05 May 2008
GGtools
supp2SQLite
EBImage
New EBImage.dll compiled with R2.7.0, GTK 2.12.9 and ImageMagick 6.4.1
Biostrings
First pass as reworking the pairwiseAlignment infrastructure to use less memory. It is also marginally faster as well.
spkTools
Adding vignette
GGtools
new support function
improved supp2SQLite
make sure it orders chromsomes suitably
EBImage
New EBImage.dll compiled with R2.7.0, GTK 2.12.9 and ImageMagick 6.4.1
ShortRead
Revised sample data
Revised sample data
AlignedRead class
- class definition
- AlignedDataFrame, extending AnnotatedDataFrame, for additional
alignment information
files) into XStringSet objects
clean generic to trim non-nucleotide sequences
CMA
Adds CMA to the 2.3 bioconductor repository.
GGtools
minor changes to getAlleles for robustness
tweak plot_EvG which can generate a dataframe in an inopportune point
ShortRead
'scripts' directory
CMA
Adds CMA to the 2.3 bioconductor repository.
affxparser
moved the updates from release to devel
LPEadj
changed version to 1.0.0
xcms
Migrate to ncdf for xcmsRaw.write()
changed part about xcmsRaw return value. via Colin
arrayQualityMetrics
- add argument grouprep for group representation. It allows to show the
boxplots and densityplots with colours according to their biological
group defined in intgroup.
[/arrayQualityMetrics] permanent link
Fri, 02 May 2008
GGtools
tweak plot_EvG which can generate a dataframe in an inopportune point
flowClust
update README instructions for Windows users; move README to inst directory
limma
Reversing changes committed in error to plots-ms.R on 9 March 2008.
Biobase
AnnotatedDataFrame made more friendly to subclassing
- previously, a subclass would often be coerced to AnnotatedDataFrame
during, e.g., subsetting
combine,matrix,matrix-method bug fix
- non-overlapping rows and columns in the second matrix were NA,
rather than the value in the second matrix
- typo in vignett
flowClust
update README instructions for Windows users
minor change to Makevars.win
limma
Reversing changes committed in error to plots-ms.R on 9 March 2008.
flowCore
fixed some typos
more specific about sotware imports now
manuscript.tex now holds the actual paper
illustration and citation
Biostrings
Better fix for adjacentViews.
Fixed a bug in adjacentViews to allow the handling of character vectors.
CGHregions
Adds CGHbase and CGHregions to Bioc 2.3 repository.
LPEadj
Added LPEadj to Bioc 2.3 Repository.
plateCore
Working on making a density plot for flowPlates.