Browse code

added novel method and increase version to 1.99

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ROntoTools@116328 bc3139a8-67e5-0310-9ffc-ced21a209358

Calin Voichita authored on 15/04/2016 05:40:35
Showing 1 changed files
... ...
@@ -1,3 +1,8 @@
1
+VERSION 2.0.0
2
+--------
3
+
4
+* added a novel pathway analysis method based on the primary dis-regulation of the genes in each pathway
5
+
1 6
 VERSION 1.2.0
2 7
 --------
3 8
 
Browse code

bug fixes and new feature to consider pathways with no interactions (i.e., gene sets)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ROntoTools@80800 bc3139a8-67e5-0310-9ffc-ced21a209358

Calin Voichita authored on 26/09/2013 16:41:14
Showing 1 changed files
... ...
@@ -1,3 +1,8 @@
1
+VERSION 1.2.0
2
+--------
3
+
4
+* add the ability to analyze gene sets (pathways with no interaction) using only over-representation
5
+* bug fixes: plot boundaries, etc.
1 6
 
2 7
 VERSION 1.0.0
3 8
 --------
Browse code

Add BaseSpaceR CNORfeeder eiR and ROntoTools to the repos.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ROntoTools@74711 bc3139a8-67e5-0310-9ffc-ced21a209358

Marc Carlson authored on 22/03/2013 22:40:44
Showing 1 changed files
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