Commits

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Author Commit Message Labels Comments Date
Qian Zhu
Include Casey's changes Remove comments and debugging code
Qian Zhu
Added SeekPValue for calculating signficance of retrieved genes Adjusted PCLServer to use Sleipnir's pearson calculation seekquery - if query size is less than # of folds of CV, should adjust the folds to query size seekcentral - clear rank vector before weighting dataset seekevaluate - enforce stable sorting, if two genes have the same score, use their entrez gene id as secondary sorting field
Casey Greene
update combiner documentation, this closes issue #21
Casey Greene
adjust lines as descibed in issue #24, this closes issue #24
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
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