flowViz
lpolygon methods now return the gate outlines and the contour function is fixed
[/flowViz]
permanent link
flowCore
added parameters method for filterResults
Changed the introduction a little and added a few sentences about plateCore.
[/flowCore]
permanent link
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.
[/Biostrings]
permanent link
Rintact
i have added the man page
i have added a new method to the package
[/Rintact]
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annotate
Changed useHomology vignette so it won't interfere with build. Will replace with a new version soon.
[/annotate]
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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
[/Biostrings]
permanent link
vsn
I added a section to the vignette about the relationship between vsn
parameters and the additive-multiplicative error model.
[/vsn]
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ontoTools
ok
[/ontoTools]
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xcmsGUI
This just creates an empty project for xcmsGUI
[/xcmsGUI]
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arrayQualityMetrics
Correcting the legend when using grouprep =TRUE
[/arrayQualityMetrics]
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oligoClasses
Bug fix: initialize for SnpCopyNumberSet
[/oligoClasses]
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flowCore
small work on the text and add references
[/flowCore]
permanent link
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.
[/Biostrings]
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BiocCaseStudies
cleaned up Description
[/BiocCaseStudies]
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GGtools
supp2SQLite
[/GGtools]
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EBImage
New EBImage.dll compiled with R2.7.0, GTK 2.12.9 and ImageMagick 6.4.1
[/EBImage]
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Biostrings
First pass as reworking the pairwiseAlignment infrastructure to use less memory. It is also marginally faster as well.
[/Biostrings]
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spkTools
Adding vignette
[/spkTools]
permanent link
GGtools
new support function
improved supp2SQLite
make sure it orders chromsomes suitably
[/GGtools]
permanent link
EBImage
New EBImage.dll compiled with R2.7.0, GTK 2.12.9 and ImageMagick 6.4.1
[/EBImage]
permanent link
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
[/ShortRead]
permanent link
CMA
Adds CMA to the 2.3 bioconductor repository.
[/CMA]
permanent link
GGtools
minor changes to getAlleles for robustness
tweak plot_EvG which can generate a dataframe in an inopportune point
[/GGtools]
permanent link
ShortRead
'scripts' directory
[/ShortRead]
permanent link
CMA
Adds CMA to the 2.3 bioconductor repository.
[/CMA]
permanent link
affxparser
moved the updates from release to devel
[/affxparser]
permanent link
LPEadj
changed version to 1.0.0
[/LPEadj]
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xcms
Migrate to ncdf for xcmsRaw.write()
changed part about xcmsRaw return value. via Colin
[/xcms]
permanent link
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
GGtools
tweak plot_EvG which can generate a dataframe in an inopportune point
[/GGtools]
permanent link
flowClust
update README instructions for Windows users; move README to inst directory
[/flowClust]
permanent link
limma
Reversing changes committed in error to plots-ms.R on 9 March 2008.
[/limma]
permanent link
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
[/Biobase]
permanent link
flowClust
update README instructions for Windows users
minor change to Makevars.win
[/flowClust]
permanent link
limma
Reversing changes committed in error to plots-ms.R on 9 March 2008.
[/limma]
permanent link
flowCore
fixed some typos
more specific about sotware imports now
manuscript.tex now holds the actual paper
illustration and citation
[/flowCore]
permanent link
Biostrings
Better fix for adjacentViews.
Fixed a bug in adjacentViews to allow the handling of character vectors.
[/Biostrings]
permanent link
CGHregions
Adds CGHbase and CGHregions to Bioc 2.3 repository.
[/CGHregions]
permanent link
LPEadj
Added LPEadj to Bioc 2.3 Repository.
[/LPEadj]
permanent link
plateCore
Working on making a density plot for flowPlates.
[/plateCore]
permanent link
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