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NEWS
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NEWS
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**************************************************
* *
* 2.0 SERIES NEWS *
* *
**************************************************
CHANGES IN R VERSION 2.18
NEW FEATURES
o release version to GitHub
CHANGES IN R VERSION 2.17
NEW FEATURES
o Added Exon and Transcript access
o Added Exon and Transcript to Mutation plot
CHANGES IN R VERSION 2.16
NEW FEATURES
o Fix consistent color usage by sorting colors based on disease types
o Fix check warnings
o Added exported get directory functions for tests
CHANGES IN R VERSION 2.15
NEW FEATURES
o Fixed issue with space and legends in mutation plots.
o Name change
o Better logging for plotting Methylation 450 data
o changed from heatmap.2 to heatmap.3
CHANGES IN R VERSION 2.14
NEW FEATURES
o Fixes to 2.13
CHANGES IN R VERSION 2.13
NEW FEATURES
o V2 AssayPlot Add Gene to Axis Labels
o V3 Add Gene Length to Mutations Title
o V3 Meth27: Single Probe Makes Ugly Heatmap
o Platform files read using C++ based package (speed and memory fix)
o Added mutation details support
o Change to DNA and Amino Acid plots for mutation plots
CHANGES IN R VERSION 2.12
NEW FEATURES
o handle new format for HG18/19 mapping files (mutation and SNP6 genomic annotation data)
CHANGES IN R VERSION 2.11
NEW FEATURES
o Use ZIP file for data
o Use package for JAR files
CHANGES IN R VERSION 2.10
NEW FEATURES
o Handle heatmaps with all NaN
CHANGES IN R VERSION 2.9
NEW FEATURES
o Add mutation data
o Add plotAssays
o Add logging and resetting of cached data by exceptions
o Add documentation on getMetadata_Gene list of lists
o Handle plotProbe and plot_GeneSymbol for methylation gracefully
CHANGES IN R VERSION 2.8
NEW FEATURES
o Add getContrast
o Add getImputedNAs
CHANGES IN R VERSION 2.7
NEW FEATURES
o updated docs
o add geneSymbolsForDataset
o add caching of values on Java side
o add JUnit tests on Java side
o geneSymbolsMatchDataset
o add getSynonyms
o export and document plotGenericOutput and plotHeatmapOutput
CHANGES IN R VERSION 2.6
NEW FEATURES
o add one-to-one ucsc/hgnc (getOneToOne)
o SNP6 Genomic Data, Objects, and Neighbors (HG18 and HG19 genomic data)
o mir Genomic Data, Objects, and Neighbors (HG19 genomic data)
CHANGES IN R VERSION 2.5
NEW FEATURES
o RNASeqV2 Gene Metadata
o RNASeq Gene Metadata
o RNASeqV2 Gene Neighbors
o RNASeq Gene Neighbors
CHANGES IN R VERSION 2.4
NEW FEATURES
o revisit colors – darker for SARC for example
o make replicate plots optional
o update docs
o getData take vector or string
o add Delta option to readGeneList functions
o add type checking
o getMetadataProbe take vector or string
o getNames_ProbeFromGeneSymbol take list or string
o add chromosome argument to ProbeByNeighbor
CHANGES IN R VERSION 2.3
NEW FEATURES
o return probe names() only for actual lists
CHANGES IN R VERSION 2.2
NEW FEATURES
o added name slot for probes, ProbesByNeighbor and other probe functions includes probe name in names()
CHANGES IN R VERSION 2.1
NEW FEATURES
o remove warnings when checking to create directory
o annotations Tissue Type name
o annotations disease name
o annotations dataset name
o add getDataObject save as list flag
o fix issue with plot delta
CHANGES IN R VERSION 2.0
NEW FEATURES
o New API and Lexicon