Commits

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Author Commit Message Labels Comments Date
chuttenh
[svn r107] Add Clusters2Dab for preclustered data conversion Fix a bug in KEGG parsing to properly gloss terms with multiple IDs Add better non-ID feature retrieval to PCLs
chuttenh
[svn r106] Add hypergeometric distance measure for binary data to Distancer/libBioUtils
chuttenh
[svn r105] Add support for multiple organisms to KEGG parser through OntoShell Add GO term gene hit output to OntoShell find command Improve Pearson correlation efficiency Fix normalized Pearson calculation for boundary cases Fix memory leak in MEFIT Add gene list opening limited to a preexisting genome Add inference algorithm switching to BNEvaluator
chuttenh
[svn r79] Add progress messages to MEFIT Fix a few Linux compatibilities in MEFIT
chuttenh
[svn r78] Fix entanglement of PNL and Smile libraries
chuttenh
[svn r77] Fix line length limit in KNNImpute Fix missing header in CFullMatrix
chuttenh
[svn r76] Add MEFIT binary for end-to-end Bayesian microarray integration Add CMeta::Deextension to strip a file extension from a string Fix the fact that PearNorm maps 1.0 to infinity (and thus missing) Add a weird workaround in Smile for the _invalid_parameter_noinfo symbol Add dat file opening from positive gene lists plus a negative set Add Smile naive network construction from a list of IDs and quants Add quant modification to data pairs Add CDatasetCompact opening…
chuttenh
[svn r75] Add a minimum score cutoff to Distancer
chuttenh
[svn r73] Add BNEvaluator for evaluation of every hidden BN node over single gene data Add partially working Renamer for human gene ID management Fix trailing tab issue (replaced by 0s rather than imputed) in KNNImpute Add whole Bayes net evaluation to libBioUtils CBayesNet classes Add partial gene name management classes to libBioUtils Add a whitespace trimming function to libBioUtils CMeta Add a PCL pair class to manage per-gene data with quantification
chuttenh
[svn r71] Add customizable background to annotations/TermFinder/OntoShell Fix boundary case bug in CMath::LogFact calculation Add beginnings of PCL-based dat file opening Update Dat2Dab to use PCL-based dats Update Clusterer to use gengetopts
chuttenh
[svn r70] Fix some Linux issues in BNTruster Add geometric and harmonic means to Combiner Fix a missing value bug in libBioUtils pearson correlation measure
chuttenh
[svn r68] Add method (max/mean) and subset command line arguments to Combiner
chuttenh
[svn r67] Add CPT accessor to Bayes net classes Add sums/ratios trust methods to BNTruster
chuttenh
[svn r66] Fix a bug in Combiner that was misaligning genes in large data sets Add an everything flag to BNTester that will keep pairs without answers Fix a typo in Sigmoider that was flipping parameters incorrectly Fix a bug in CDatasetCompact that was mangling the everything flag
chuttenh
[svn r64] Improve Pearson correlation to ignore missing values Improve CStatistics Average and Variance to use better templating Add mean/stdev normalization to CPCL (and rearrange header a bit) Add Dat2Graph front end to the previously added CDat graph output Add PCL normalization front end to Normalize Add SQL table output to BNFunc
chuttenh
[svn r63] Fix pointer-based OpenToken to avoid running off the end of the string Add minimum correlation cutoff to MCluster/CClustHierarchical Improve PCL opening to avoid all of those awful stream/token/linebreak checks Add graph output (in several formats) to dat files
chuttenh
[svn r62] Add everything flag to Dab2Dad and compact dataset construction Fix PCL gene addition to align new features
chuttenh
[svn r61] Add default CPTs to SMILE Bayes nets for naive learning Update hierarchical clustering to MeV algorithm (much faster!) Add row expansion to full matrices/PCL files Fix MCluster to correctly deal with genes missing from the PCL Add skeleton (unimplemented) Gaussian mixture fitting to functional Bayes nets Improve text dat file opening (what was I thinking??)
chuttenh
[svn r60] Add normalization flag to Dat2Dab Fix Linux static linking for BNTester, BNConverter, BNTruster Fix Answerer to ignore empty functions Fix a typo in the functional Bayes net learner Update the SMILE Bayes net learner to smooth missing data from adjacent columns
chuttenh
[svn r59] Add exponential nodes to functional Bayes nets
chuttenh
[svn r58] Fix unnecessary (or harmful) unsigned int casts
chuttenh
[svn r57] Add beta distribution to CStatistics Update CDataset to load quantized files whenever possible Fix all of the functional Bayes net learning/evaluation stuff Add Gaussian and beta function BN learners
chuttenh
[svn r56] Safekeeping checkin before ripping apart CDataset Update CDataset and CExampleImpl to handle continuous data better Add per-node continuous/discrete checking to Bayes nets Add answer-less CDataset opening Add function-fitting Bayes net class CBayesNetFN Add CBayesNetFN access to BNConverter and BNTester
chuttenh
[svn r55] Add implementation for the -t testing argument of Answerer
chuttenh
[svn r54] Add z-score normalization to Normalizer Fix Answerer behavior under Linux Add Makefiles for BNTruster and DSLConverter Update Combiner to max rather than average Fix dat gene list Open method to not overwrite positives
chuttenh
[svn r53] Add GetGeneNames to libBioUtils CGenome Add Answerer to generate answer files from gene lists Add gene list Open method to libBioUtils CDat Update BNTruster to take the network prior into account
chuttenh
[svn r52] Add single datum evaluation to libBioUtils Bayes nets Add BNTruster to evaluate per-node BN posteriors Add DSLConverter to interconvert (X)DSL files
chuttenh
[svn r51] Add proper negative pair functional handling to DChecker and WilcoxonRankSum Fix diagonal lookup in binary half matrices
chuttenh
[svn r50] Update Combiner to take advantage of more memory (not use subsets) Update DChecker to use inverted AUC when requested Fix libBioUtils CDatasetCompact on 64-bit machines with -1s Add invertable AUC to libBioUtils CStatistics
chuttenh
[svn r49] Improve GO annotation parsing to relax and allow human annotations Add gene inclusion list to Wilcoxon rank AUC
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