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Author Commit Message Labels Comments Date
Chris Park
removed automake *.am files
Chris Park
add to ignore *.o files
Chris Park
modified a bug that used 'dmissing' flag checking with "_arg" instead of "_given"
Actually added PCL2Bin files
-Added memory mapping support for pcl files
Chris Park
merge annotation OBO updates, plus PR/RECALL columns to DChecker
Chris Park
merge Hypergeometric clarifications
Chris Park
merge support of 'bin' binary PCL files
Chris Park
merged qdab support and additional functionalities for Dat2Dab
Chris Park
added .hgignore to ignore deps cache Po etc generated files
KEGG no longer wraps lines so a substantially larger buffer size is now needed for lines from the ko file.
Make memory mapping of output files optional via -M flag. This flag affects the inference mode and should only be used if you have sufficient local storage for intermediate networks. Without this flag, it is best to have sufficient RAM for intermediate networks.
Chris Park
Added new tool MIed, similar to MIer however calculates MI between two dataset only using the union of the two gene sets. In contrast, MIer uses the sum of all genes among all datasets given to calculate MI. MIed allows MI to be constant even after adding new dataset into the integration.
Curtis Huttenhower
Fix bug in CDat::Open( CDat, vector<CGenes>*, ... ) for importing known negatives
Improve COALESCE termination criteria (slightly more permissive)
Divided the code execution in two different stages: training and prediction
Seperated the execution in two stages: Training and Learning
- Modified joint probability computation between the species.
Updated SpeciesConnector removing Gibbs sampling.
Fixed SpeciesConnector to execute mkdir in UNIX.
Fixed Dat2Dab.cpp: Test for -1 rather than 0 for checking missing values.
Fix build scripts to pick up extlib dependencies
Update documentation to include new email and Mercurial repo location
Add covariate mutual information approximation to Counter
Curtis Huttenhower
Remove obsolete VS2005 project files
rmcg:00408: merged changes to boost and build script
rmcg:00408: added hg update to nightly build/make script
Fix push hook script to remove temporary file, avoiding permissions errors
Add new boost regexp library to BOOST_LIBS along with graph library
adding script directory back in
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