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Bioconductor Changlog.
Tue, 13 Oct 2009
KEGGgraph
version 1.1.5: dependence on Rgraphviz is set to 1.22.0
KEGGgraph
format fix: invalid whitespace in item is fixed
KEGGgraph
Version bumped to 0.8.7: pdf vignette added, plotKEGGgraph function with new paramter 'nodeRenderInfo'
plotKEGGgraph adds nodeRenderInfo parameter
KEGGgraph
Adds KEGGgraph to the repository.
KEGGgraph
KEGGgraph 0.8.16: in case SPIA package is not available the backup data will be loaded in the vignette from KEGGgraph package. This is only for the beta-phase
KEGGgraph
KEGGgraph Update Version 1.1.1: improved render of KEGG pathway graphs with new interface of Rgraphviz
KEGGgraph
update to 0.8.14
Explains how to retrieve KGML files remotely
Get rid of underscores to avoid Windows version crash
adding KGML files for merging
Introducing how to retrieve KGML file remotely
KEGGgraph
neighborhood returns unique restuls
Upgrade to 0.8.9
Add neighborhood method: to extract neighborhood set of given node(s)
KEGGgraph
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
KEGGgraph
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
KEGGgraph
version bumping to 0.8.13. The last update before the next release
add translateKEGGgraph and its helper functions
update plotKEGGgraph function to be able to plot translated pathway graphs
version bumping
getDisaplyName does not stop if the display name cannot be found, it just fill the not-found names with the raw node name
version bumping
queryKEGGsubgraph uses subKEGGgraph function instead of subgraph function to subset the node/edge information too
updated vignette, spelling fixes
version bumping
updated vignette
obsolete help files
add function 'queryKEGGsubgraph' to query subgraph of a KEGG graph with given genes as nodes
annotation functions moved annotation.R
KEGGgraph
Bumping the version number for the upcoming release.
KEGGgraph
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
KEGGgraph
updated the note of retrieveKGML file for windows users. Thank the report and discussion from Takeshi Nishiyama, National Insitute of Public Health in Japan
KEGGgraph
XML news did not specify the change of xmlChildren exactly, therefore a relative new version (2.3) is used.
debug of parseKGML: change of XML package (xmlChildren returns list() instead of NULL in case of no children) raised issue solved. Thanks the report and fix of Matt Settles (Washington State University), and the report of Yongjin Li. Working version 1.1.2
KEGGgraph
queryKEGGgraph uses addNode from graph package, which was not specified before. It could have led to bug in case the graph library is loaded before the KEGGgraph. The bug is solved in the version 1.1.10 by David
KEGGgraph
Version 1.1.3: (1) from now on devel-versions ALWAYS end with odd numbers, while stable versions have even tailing number (2) inconsistent documentation in KEGGNode and KEGGEdge class is corrected
KEGGgraph
omitting the nondetected nodes from up-regulated gene figure
fix SPIA and hgu133plus2.db depends names
version to 0.8.15: adding KEGGgraphApp vignette, demonstrating to use KEGGgragh to parse newly created or edited pathway, and to cooperate with other packages to analyze data
adding KEGGgraphApp vignette
adding xml files for application example
KEGGgraph
suggests org.Hs.eg.db for ID conversion example in the vignette; version bumped to 0.8.8
updated vignette: examples of ID conversion with org.Hs.eg.db, ackowledgement added
add examples to convert ID with org.* packages; add acknowledgement
KEGGgraph
textit macron all removed since Rdversion 2 parser does not recognize them for now
KEGGgraph
version bump to 1.1.9: KEGGgraph software supports multiple substrates/products in KGML reaction from version 1.1.9.