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, 22 May 2008
AnnotationDbi
Adds new Ensembl mappings to mammalian org packges.
Mouse, Rat and Human now can support Ensembl transcript IDs, these IDs
are availaible in new mappings and documented. The mappings for mouse
Ensembl protein IDs have also been added with this patch (previously
only MGI IDs were in place in the mouse).
[/AnnotationDbi] permanent link
limma
22 May 2008: limma 2.15.5
- fix bug introduced to plotMA() in version 2.13.6: plotMA()
ignored array argument when object was of class RGList.
Correct function now restored.
hexbin
updated hexplom, plus several adjustments
update to hexbinplot to bring it more in line with recommended practice when writing lattice extensions
ShortRead
doc tweaks
code tidy
srsort, srorder, srduplicated
- sort, order and identify duplicate string sets and quality scores
Biostrings
Added a new qualitySubstitutionMatrices function for quality adjusted alignments.
Bumping the version number so recent changes will be included in next build.
Adding a new compareStrings function for looking at aligned strings.
Added an inserts accessor method for AlignedXString class.
Fixed a bug in the profile calculation in pairwiseAlignment.
Made alignScore function defunct.
Fixed two bugs in pairwiseAlignment, one in the traceback procedure and one when there is no alignment.
annotate
some stuff for pubmed-based literature page generation
affxparser
Fixed up writeTpmap as per bug report on BioC
Biobase
NEWS for makeDataPacakge
makeDataPackage gets a 'description' argument
sample.ExpressionSet abstract now claims correctly to be ExpressionSet