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, 02 Jul 2009
Biostrings
Use closest integer mismatch in trimLRPatterns when mismatch parameter is in (0,1).
GGtools
pass chk
minor import change
RmiR
Change to use RmiR.Hs.miRNA
CAMERA
Fix getpspectra(), now using same colnames as originat xcmsSet, instead of hardcoded ones
ShortRead
the 'coverage' instead of the 'pileup' function and hence works
with 'Rle' vectors throughout.
HilbertVis
changed shrinkVector and plotLongVector to support Rle vectors
Fixed to minor typos.
updated vignette to mention that hilbertDisplay now supports Rle vectors
arrayQualityMetrics
Correct the matching of slots between R code and man pages
[/arrayQualityMetrics] permanent link
BSgenome
gdreduce, 'Reduce' sereral GenomeData or one GenomeDataList to GenomeData
IRanges
Minor code changes to coverage calculation to provide minor speed ups.
Sped up coverage execution for IRanges objects.
Fixed man page to agree with code.
Removed extra } from man page.
Added missing closing } in man page.
Update chain file reading for new List infrastructure.
RangedData now automatically coerces its first argument to a
RangedData, if it's not a Ranges. Add coercion from
data.frame/DataTable to RangedData.
rtracklayer
The error handler in the HTML parser now allows for an empty 'level' argument.
Support coercion of first argument in GenomicData. Rename 'chrom' to
'space' for data frame objects.
Tweak demo and vignette.
Ensure scores are numeric in BED output.
plateCore
Working on man pages and commenting code.
Working on man pages and commenting code.
Working on man pages and commenting code.
Removed all data driven normFilter gates from examples to decrease R CMD check runtime.
Reduced size of sample data set, ran vignette again.
Reduced size of sample data set.
Cleaning up errors from R check
Cleaning up errors from R check
Fixed problem matching sampleNames in plotPlate
Fixed problem matching sampleNames in plotPlate
Fixed a bug in fpbind that was causing problems merging identical plates.
Fixed a bug in fpbind that was causing problems merging identical plates.
Cleaning up errors from R check
Cleaning up errors from R check
Fixing R CMD Check problems.
Fixing R CMD Check problems.
Fixing R CMD Check problems.
Fixing R CMD Check problems.
Fixing R CMD Check problems.
Fixing R CMD Check problems.
Fixing R CMD Check problems.
Fixing R CMD Check problems.
Trying to get package in shape for release. Updating man pages
Trying to get package in shape for release. Updating man pages
Trying to get package in shape for release. Updating man pages
Updating plateCore vignette
affycoretools
Added imports(AnnotationDbi, get) so things like get(goid, GOTERM) will work.
[/affycoretools] permanent link
CNTools
A bug fix on the mapping of segment value to genes
crlmm
update computeCopynumber, added .R files for new classes/methods
Rgraphviz
Fixed a configure bug, updated README
flowStats
fixed some bugs in peakSeperator.R and landmarkMatrix.R.
fixed a bug in landmarkMatrix.R.
bumped up version number to 1.3.8
Fixed function pruneRegions -- if the areas of the polygons are too
small, then do not collapses them.
edited gpaSet's man page
edit gpaSet's man page
Added an example in gpaSet.R using normalization object and work flow.
HilbertVisGUI
- hilbertDisplay and hilbertDisplayThreeColor now accept
Rle vectors (from IRanges)
- hilbertDisplayThreeColor now deals more sensibly with
data of different length
- the GUI understands the mnemonic keys Alt-P and Alt-N to
cycle through the data vectors
[/HilbertVisGUI] permanent link
cghMCR
Minor change to the plot function
Smaller sample data replaced the large ones.
One more large file removed
Large data files removed
beadarraySNP
Handle missing data in report files in function read.SnpSetIllumina()
[/beadarraySNP] permanent link
iFlow
adding normal menu
again
playing
fix bugs
fix bugs
ArrayExpress
Replace sampleNames(dat) by sampleNames(dat) for NChannelSet
[/ArrayExpress] permanent link
flowUtils
storing tag defaults in an xml file now
changing extension to capital R and adding dependcies
Adding functionality to write FlowJo workspaces from workflow objects
Deleting Emacs temp file that were checked in
biocViews
Save data in sqlite2 format.
Added DNACopyNumber to the biocViews ontology.
flowCore
Fixed issue with the wrong min range when reading in a fcs file , bumped version no
making sure the range parameter is ignored for clipping after the data has been transformed
AnnotationDbi
Overloads the Term and related methods for GOTERM
This update overloads the Term, Ontology etc. methods for GOTERM so
that they can take IDs or GOTermsAnnDbBimap.
[/AnnotationDbi] permanent link
Sun, 28 Jun 2009
affycoretools
Small fix to hyperGoutput. The output of annotation(GOHyperGResult) no longer contains the .db suffix, so this has to be added back on.
[/affycoretools] permanent link
Sat, 27 Jun 2009
EBImage
fixed noGTK support
minor
fix noGTK support in display.c
cghMCR
Vignette modified and SGOL algorithm and sample data added.
plateCore
Updating plateCore vignette
Cleaning up plateCore files, getting ready for release.
affyPara
error in justvsnPara removed
Biostrings
Bumped version to 2.13.22 in order to release the new code for fast matching of the head/tail of a PDict object. In some situations where the head/tail is very narrow (<= 8b in total), the overall speed up for matchPDict() can be 10x or more.
flowFP
Edited the man page for flowFPModel to indicate that a flowSet is collapsed to a flowFrame for binning.
Minor changes to the vignette to show the use of named parameters in addition to numbered parameters.
Previous change bumped version.
Fixed bug in flowPlex construction. Checks the number of instances as well as
the sample names of each instance for consistency.
Added excludeTime (default TRUE) to the model constructor so that if the user
want to consider all of the parameters in an fcs file, the constructor will
attempt to exclude the parameter containing time, if it is found.
Added 'bin_cols' to model plotting, allowing the user to supply colors to the
plotted bins, for model plotting.
Removed '<' symbol from the 'qc' and 'fancy plot color legend.
Removed references in the make system, (configure.ac) to BLAS and the gsl
library.
Removed aclocal.m4 file which is no longer needed.
KEGGgraph
version bump to 1.1.9: KEGGgraph software supports multiple substrates/products in KGML reaction from version 1.1.9.
bioDist
improved implementation of KLdist functions
ROC
minor changes to doc and enhanced selection of C interface for dxrule.sca
crlmm
added classes/methods for intermediate files and copy number analysis; added wrapper for preprocessing and genotypes.
globaltest
- fixed a bug in inheritance() sometimes causing a unended processing of the function.
- removed redundant levels in factor response in gt()
- transpose option fixed
- fixed the possibility of providing weights as a list of named vectors
EBImage
new installation in inst/doc
plateCore
updated the isogates function so that you can ignore the low values if you want.
there is now an argument minCut=NULL. when it is NULL, then nothing is done and so existing results won't be changed. If you supply an argument, typically 10, then these values will be omitted when calculating the percentiles.
comments on paper and reviewers
XDE
added seed to XdeParameter-class man page