Commits

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Author Commit Message Labels Comments Date
Casey Greene
more code cleanup, try to read quants *before* dabs (saves significant time with MIer, particularly with valgrind running), improved table output
Casey Greene
remove old debug code
Casey Greene
This clarifies the MIer documentation and closes issue #5
Casey Greene
subsample code comparison was reversed, this closes issue #23
Casey Greene
parallel MIer with openmp, major code cleanup, only do stuff related to MI if we actually need it (i.e. not for other measures)
Casey Greene
automatic whitespace correction via vim
Casey Greene
Allow MIer to load the datasets once if enough RAM is available (command line option)
Casey Greene
astyle --style=stroustrup, address style/indentation inconsistencies
Casey Greene
one last gcc 4.7 fix
Casey Greene
update everything that builds before SVMperfing for gcc 4.7 unistd.h change (see: http://gcc.gnu.org/gcc-4.7/changes.html )
Casey Greene
Add missing binaries to configure.ac.
Casey Greene
add gsl to ubuntu instructions to match qian's changes
Qian Zhu
Merge
Qian Zhu
Added functionality to calculate average query-query correlation
Chris Park
Added function to do a user defined weighted combination of dabs
Chris Park
SVMperfing added option to sample gold standard Added two new tools: SparseNetCombiner lets you combine multiple dabs that are sparse and may have different gene order but still same set of genes (NetworkCombiner requires fully connected network with same gene order) NetMiner will be continuously developed to ultimately mine directed steiner trees in gene networks, currently just allows you to query genes in a dab.
Aaron Wong
Fix obo, remove debug
Aaron Wong
Merge
Aaron Wong
Remove debug; alternative float array for storing edge scores
Qian Zhu
Refine search datasets if some search datasets are found to contain no query genes.
Qian Zhu
merge
Qian Zhu
seekcentral: added pseudo (or simulated) weight option for equal weighting, order-statistics algorithms seekdataset: added option to randomize of data (for permutation test) SeekServer: added option to specify algorithm, algorithm parameters
Qian Zhu
Fixed bug in GSL library detection (see src/Makefile.am)
Aaron Wong
remove debug
Aaron Wong
merge
Aaron Wong
Add on-the-fly inference to BNServer; fix bug when initializing nibble flag
Aaron Wong
Fix 1-index of genes (BNServer is 1-based, CDatabases 0-based)
Aaron Wong
Allow multi-gene queries
Aaron Wong
Added on-the-fly option that performs inference with a given list of bin effects and a query gene
Aaron Wong
Add checks for input args to BNServer
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