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Author Commit Message Labels Comments Date
Curtis Huttenhower
Add full meta-analytic CDat combination to Combiner Equivalent to weighted mean; should be used with z-score normalization Seems to perform almost identically to unweighted and is ~4-6x slower Add the long-awaited ability to do non-discretized comparisons (poorly) in MIer Add genewise context inference (multithreaded) to Counter Add CDat::Clear function to initialize non-NaN values Fix some gcc floating point compilation glitches in CPCL and Fu…
Tags
v1.00326
chut...@hutlab3.sph.harvard.edu
Add AUCn scoring to DChecker (AUC for first n negatives) Add "diff" subtraction combination and missing value zeroing to Combiner Add heuristic CPT-based regularization to CBayesNetFN (crummy) Update Clinician so that interaction network is optional Add dynamic gene addition to CDat/CHalfMatrix Fix missing SIZE_MAX on some Mac OS X versions (thanks Alice Koechlin!)
chut...@hutlab3.sph.harvard.edu
Add per-gene weights to HEFalMp/bioPIXIE queries in CDat Improve CDat::SaveDOT edge coloration (by z-score rather than 0-1 scaled) Improve COALESCE convergence when performing dataset blocking Improve Dat2Graph query weighting and edge normalization Add column sum normalization to CPCL and Normalizer Fix Answerer documentation - thanks to Arjun Krishnan! Fix Cliquer bug in edge exclusion for non-zero-one scaled networks Fix Funcifier calculation to acco…
chut...@hutlab3.sph.harvard.edu
Fix a documentation typo in the 2.1 release notes
chut...@hutlab3.sph.harvard.edu
Fix typo in CGenes::Open
eb...@Eric.bluefuzzball.org
Update documentation for v2.1
chut...@hutlab3.sph.harvard.edu
Add per-column frequency weighting to Distancer and CPCL::Distance Weights similarity measure by fraction of rows with values Fix Combiner absolute reweighting Add edge-specific filtering to Dat2Dab Add output z-score normalization to Funcifier Fix Hubber calculations to be more accurate/efficient/comprehensive
chut...@hutlab3.sph.harvard.edu
Add absolute weighting to Combiner Add Linux build for Clinician Fix Hubber hubbiness calculation for sparse networks
eb...@Eric.bluefuzzball.org
Add Clinician tool for multiply testing variables against gene expression Add AddGene to CGenes Fix CMeasureBinaryInnerProduct to be sensitive to missing values Fix Hubber's standard deviation of cliquiness calculation
chut...@hutlab3.sph.harvard.edu
Add several missing header includes Fix minor edge case bugs in CCompactMatrix, CDatImpl Add inverse DAT combination to Combiner (terms->genes) Fix gene lookup output in Dab2Dad Add randomization to Dat2Dab and CDat Add mutual information to Distancer Add better gene filtering to Hubber and fix some numerical issues
chuttenh
Add gene and term filtering to Combiner Add manual cluster seeding to COALESCE Fix typo in CPCL MedianMultiples
chuttenh
Fix a dumb bug in Filterer having to do with negative range specification
chuttenh
Merge
chuttenh
Merge
chuttenh
Merge
chuttenh
Add half2 scripts and solution/project info for SMRF
chuttenh
Add Filterer project file
chut...@hutlab3.sph.harvard.edu
Fix COALESCE nonsense Bayesian integration now plays nice with motif scores Small numbers of motifs are upweighted, large numbers downweighted Add density sharing for smoothing of sequence motif scores
chut...@hutlab3.sph.harvard.edu
Add weighted DAT/DAB averaging to Combiner Add Filterer tool for flexible DAT/DAB filtering (by value)
chut...@hutlab3.sph.harvard.edu
Update SMILE etc. from pull
chut...@hutlab3.sph.harvard.edu
Add SMRF tool for interaction-network-based SNP reranking Fix Linux segfault with certain gcc versions Update COALESCE to use proper Bayesian probabilities, better presets
chuttenh
Update SMILE to VC 2009 Add more flexible multithreading to BNCreator Fix a few Windows and GCC 4.3 build problems Add a draft MedianMultiples implementation Funkiness! Use at your own risk Add subsampling to MIer Add more flexible PCL normalization toe Normalizer
chut...@hutlab3.sph.harvard.edu
Initial checkin; remove unnecessary tags directory
chuttenh
[svn r429] Add v2.0 tag
Tags
v2.0
chuttenh
[svn r428] Fix minor logging and Counter code consistency issues Add initial tag information for v2.0
chuttenh
[svn r427] Fix OntoShell bug in calculating indirect annotation counts Fix log4cpp static initialization to work around gcc fiasco This updates every g_CatSleipnir logging call!
chuttenh
[svn r425] Update Linux build
chuttenh
[svn r424] Add all missing documentation (primarily COALESCE and SVDer) Add off-by-default single channel normalization to COALESCE Automatically detects and log/median transforms single channel data It's slow and doesn't really improve results
chuttenh
[svn r423] Add single-channel MA normalization (off by default) to COALESCE
chuttenh
[svn r422] Add Linux build and tweaks for SVDer
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