git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ROntoTools@116328 bc3139a8-67e5-0310-9ffc-ced21a209358
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ROntoTools@80800 bc3139a8-67e5-0310-9ffc-ced21a209358
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ROntoTools@74711 bc3139a8-67e5-0310-9ffc-ced21a209358
1 | 1 |
new file mode 100644 |
... | ... |
@@ -0,0 +1,25 @@ |
1 |
+ |
|
2 |
+VERSION 1.0.0 |
|
3 |
+-------- |
|
4 |
+ |
|
5 |
+Initial release of package ROntoTools includes: |
|
6 |
+ |
|
7 |
+* pe: Pathway analysis tool Pathway-Express with the following features: |
|
8 |
+ - perform pathway analysis on pathways defined in the standard graph format |
|
9 |
+provided by the package graph |
|
10 |
+ - perform the analysis using either differentially expressed (DE) genes or |
|
11 |
+using a cut-of-free analysis |
|
12 |
+ - when available, use both information related to the strangth of the inter- |
|
13 |
+action between the genes (as edgeWeights) and the relevance of each gene (as |
|
14 |
+nodeWeights) |
|
15 |
+ - the results are summerized using the generic function Summary |
|
16 |
+ |
|
17 |
+* keggPathwayGraphs/keggPathwayNames: Utility to download and parse the KEGG |
|
18 |
+pathways data in graph objects: |
|
19 |
+ - based on the work in the packages KEGGREST and KEGGgraph |
|
20 |
+ |
|
21 |
+* nodeWeigths: the missing generic convenience function from package graph to |
|
22 |
+get the node weights of a graph |
|
23 |
+ |
|
24 |
+* alpha1MR/alphaMLG: two utilites to transform the a vector of p-values into |
|
25 |
+weights to be used as nodeWeights |
|
0 | 26 |
\ No newline at end of file |