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Author Commit Message Date Builds
chuttenh
[svn r421] Add SVDer from AJ Sedgewick's JP Performs SVD-space PCL rescaling as per Matt's SPELL procedure Add CFullMatrix::SVD from AJ's JP Add motif matching algorithm selection to COALESCE PWM correlation p-value, RMSE, or Jenson-Shannon divergence Fix gene list mismatch behavior for CDat::Open from a base CDat Add proper duplicate handling to CDat::Open from a filename Fix CPCL::Normalize( ENormalizeColumn ) stdev calcuation typo Fi…
chuttenh
[svn r420] Add minimum effect size for COALESCE conditions and motifs This results in both different behavior and reorganized code Improve (maybe) COALESCE handling of all missing values Conditions with absolutely no data are ignored Improve COALESCE default command line parameters Only clusters that are complete subsets will merge Genes will be kept in they're in >=1/2 of the merged clusters Improve COALESCE wiggle track input (arbitrarily many unflagged on…
chuttenh
[svn r419] Fix PCLPlotter.ggo merge issue
chuttenh
[svn r418] Add missing motif-related ggo file updates to PCLPlotter
chuttenh
[svn r417] Remove excessive missing value warnings from CFASTA Add proper IMeasure mapping to CMeasurePearsonSignificance Fix KNN crash on missing neighbors Add ENormalizeMean to the range [0, inf] exp. 1 to CPCL Fix missing value handling in CStatistics::Percentile Add z-test sample size based scaling to CStatistics::MultivariateNormalCDF Fix handling of ties in CStatistics::WilcoxonRankSum AUC calculation Add progressive stdout updates to COALESCE Fix Count…
chuttenh
[svn r416] Fix one more potential bug in CCoalesceHistogramSet::Initialize Remove unnecessary COALESCE testing code
chuttenh
[svn r415] Fix deadly COALESCE bug in CCoalesceGeneScores::Grow Previous m_iMotifs _not_ necessarily equal to previous m_iCapacity For example, in cases of skipped/unused motif IDs This led to complete screwage (OBOs) of motif counts during Grow Fix deadly COALESCE bug in CCoalesceGeneScores::Add Genes with sequences length <k were detected as having no scores This made them sequenceless and behave incorrectly for later PST matching Add COALESCE test code for archival purposes (to be removed imminently) Add known motif parsing/tagging to COALESCE Open in standard format through COALESCE/CCoalesceMotifLibrary Detect using significant PWM correlation in CCoalesceCluster::LabelMotifs Store in ID/score pairs in SMotifMatch Add input/output in Open/Save calls Fix incorrect err… Add rudimentary known motif scanning/counting to PCLPlotter Add byte-accurate message logging to BNServer Add kmer/rc matching to CCoalesceMotifLibrary::GetMatch Not needed during normal usage, useful for testing Add cluster postprocessing from .out file(s) to COALESCE Largely untested! Update CPCL::OpenExperiments to allow zero experiments Keep an eye on this for interactions with DAB miso…
chuttenh
[svn r414] Fix a silly bug introduced by the tokenization change
chuttenh
[svn r413] Fix a few Linux burps
chuttenh
[svn r411] Add maximum motif cap for COALESCE New motifs won't be discovered past a point until cluster convergence Improve ZScore/CohensD usage in COALESCE CohensD for motifs, ZScore otherwise Add FASTA sequence length analysis and background gene lists to PCLPlotter Improve binned variance calculation in CCoalesceHistogramSet Integral over x^2 - I got to use calculus! Fix tokenization of input with nonstandard characters Update VS2008…
chuttenh
[svn r410] Add missing PCLPlotter directory
chuttenh
[svn r409] Update count matrix to short rather than char in Combiner to handle more MAs
chuttenh
[svn r408] Update svm_light to svm_perf Update all accompanying configure/Makefile/scripts/includes/etc. Fix a Linux glitch or two in CStatistics and OntoShell Update Linux cmdline.[ch] files
chuttenh
[svn r407] Fix a horrific bug in runtime COALESCE motif merging Only the first subsequence score (and no subsequent ones) was being updated Improve handling of redundant motif merges in COALESCE Improve variance calculations in CStatistics Add proper minimum edge weight filtering to DAT output in Dat2Graph
mark
[svn r405] improved gengetopt configure support, rebuilt some out-of-date cmdline files
chuttenh
[svn r404] Add cluster trimming to COALESCE Statistically unlikely genes are removed from each cluster before merging Remove effect size based probability adjustment from COALESCE Found to degrade performance in low-variance situations Improve COALESCE stdev calculations to be global rather than cluster/pot Greatly improves performance, surprisingly enough! Improve PCL normalization in COALESCE to be more user friendly Internal norm…
chuttenh
[svn r403] Fix CClustKMeans to work with missing precomputed similarity values Fix CPCL column normalization for zero stdev conditions Add negative-only listing to Explainer
chuttenh
[svn r402] Fix a dumb typo that broke PCL parsing
chuttenh
[svn r401] Fix a Linux quibble in CPSTImpl
chuttenh
[svn r400] Add recursive GetChildren and GetParents to IOntology/COntologyImpl Fix multiple parent/child annotation bug in COntologyImpl Although why GO needs to annotate genes to terms' descendants, I'm not sure Improve CFile organization (particularly OpenToken) for better performance Improve performance of CPCL::Open Add simplification trimming to CPST::RemoveRCs Only branches with frequency above 1/arity are preserved Add CPST::Integrate and CPST::Simplify Former g…
chuttenh
[svn r399] Fix a Linux-specific typo in COntologyImpl
chuttenh
[svn r398] Improve COALESCE behavior with ZScore instead of CohensD New stats fixes make the extra hoop-jumping unnecessary Fix COALESCE Subtract bug Remove only the difference against the mean, not the whole signal Fix minor COALESCE bug in per-condition stdev calculation Rounding error was causing some weird behavior in low-variance conditions Add Bonferroni correction to multivariate p-value COALESCE dataset selection Improve COntologyImpl organization fo…
chuttenh
[svn r397] Improve RC removal during PST->PWM conversion Now done by alignment rather than purine content
chuttenh
[svn r396] Fix COALESCE bug that was completely screwing up clustering statistics Only some gene/motif updates were being recorded between iterations Fix COALESCE bug involving gene set modification between clustering iterations Fix COALESCE bug in motif match weighting when no modifier tracks are given Improve COALESCE postprocessing for module with nonintersecting conditions Improve COALESCE behavior for low standard deviation Improve summation over bin centers in CCoalesce…
chuttenh
[svn r395] Fix a bug in Counter (extension location in quant files) Update Makefiles and cmdlines for Linux Add information output to Synthesizer
chuttenh
[svn r394] Improve COALESCE code organization Split into several different headers, internal headers, and source files Greatly speeds compilation times in many cases Fix COALESCE so that genes with no sequence aren't counted as zeros Improve COALESCE postprocessing algorithm Cluster similarity score improved (again) Low z-score and low information motifs are dropped RCs are removed (more or less) in PWMs PWMs are generated as inte…
chuttenh
[svn r393] Add Dab2Dad option to output all values as continuous (not quantized) from DABs Add invalid dataset index checking to Counter Add PCL validation check to Combiner Add multiple hypothesis testing to postprocessing in COALESCE Add gene name caching to Clusters2Dab Fix broken extension validation in BNWeaver Fix CPST input/output for non-unitary character counts Fix CPST alignment for PSTs of very different lengths Add PWM generation from CPST and CCoalesceMotifLibrary Add simpl…
chuttenh
[svn r392] Fix memory management incompatibility with Linux in CCoalesceGeneScores For some insane reason, deleting and newing over many pointers leaks sometimes Managing the memory as one big chunk works just fine So many float*s in a float*[] were replaced by one big float[] and offsets Fix a charming race condition in CCoalesceGeneScores The memory management thing is Linux's fault; this was all me Add a crummy approximate memory usage checker to CMeta
chuttenh
[svn r391] Update Linux build and cmdline.[ch] files Fix missing STL include line in fullmatrix
chuttenh
[svn r390] Add missing Matcher directory
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