[BioC] Recent changes to Bioconductor packages
madman at jimmy.harvard.edu
madman at jimmy.harvard.edu
Sat Apr 26 06:00:03 MEST 2003
This is an automated message sent out weekly to report recent changes
to Bioconductor packages. Please see the URL
http://www.bioconductor.org/changelog.html for a complete history.
Apr 26 2003: limma - imported version 1.0. GKS
Apr 25 2003: data packages - new data packages (1.2.1) constructed with
1. Any occurrence of AFFY has been replaced by PROBE to make the
2. Mappings to GO ids become a named vector with the name(s) being
the evidence code(s) provided by NCBI.
3. Values of GOXXPARENTS in GO package also become named vectors
with the names being either isa or partof to indicate the
relations of GO ids to their parents.
4. GO package includes GOXXCHILDREN to allow for search for direct
children and GOCATEGORY for grouping (to MF, BP, and CC)
5. Dependance of Biobase removed. JZ
Apr 25 2003: reposTools - pathed the release 1.1 branch version of
reposTools to account for the bug fixes and updates to the
package from the development branch over the last month. JG
Apr 24 2003: Iyer517 -- new package 0.1 ... time course experiment from
Science 1999 paper of Iyer in Eisen lab. Includes vignette.
May be ready for release VJC
Apr 24 2003: affy - The default background adjustment given by the rma()
function has been changed so that it agrees with the results of
expresso. If you wish to enable the previous behaviour use
bgversion=1 in your rma() call. The function just.rma() has
also been adjusted accordingly. BMB
Apr 25 2003: limma 0.9.7 - new package - Linear Models for Microarray Data.
Data analysis, linear models and differential expression for spotted
and oligonucleotide microarrays. GKS
Apr 24 2003: reposTools - Fixed several bugs, primarily one in which
the system was not always checking that the version of the package
available was newer than the current installation of a package. JG
Apr 23 2003: reposTools - Fixed a bug in the dependency checking routines,
which would appear if a user maintained multiple libraries of R
packages. The system would only check for dependency resolution
in the same library directory that the package was being installed to.
It now checks .libPaths(). JG
Apr 22 2003: Rgraphviz - Graphs can be plotted w/ twopi layout method
even if not fully connected. JG
Apr 22 2003: tkWidgets - a new function - DPExplorer - added. The function
allow users to explore a Bioconductor data package using an
interactive widget. JZ
Apr 22 2003: Rgraphviz - set up Rgraphviz to use stored images for generic
and method code via install.R much like the Ruuid package. JG
Apr 22 2003: reposTools - The default action when one specifies repositories
manually is to no longer attach any repositories from the R options.
This can be forced via 'searchOptions=TRUE'. Furthermore, when
repositories are manually specified, the system will *not* honor
previous repository information during updates. JG
Apr 20 2003: ROC no longer requires Biobase
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