Changes in version 0.99.3: o BUG ANNMAP-110 XXXInRange( NULL ) used to throw an error. It now returns NULL. o BUG ANNMAP-111 Fix crash when translation data is incorrect and causes us to fall off the translation exon when finding the UTR/Coding range. Changes in version 0.99.2: o BUG ANNMAP-109 geneToSymbol when passed a vector of gene IDs, returned the symbols in the order of the genes start location rather than the order the function was called with. Changes in version 0.99.1: o BUG ANNMAP-101 ngsBridgePlot called with no genes in range had a huge border. o BUG ANNMAP-106 Empty ngsBridgePlot trace should draw line at 0. o BUG ANNMAP-107 transcriptToCodingRange was very slow. Changes in version 0.99.0: o NEW Initial Release to Bioconductor o BUG ANNMAP-98 A call to transcriptToTranslatedprobes for transcripts in HPRT1 caused a crash Changes in version 0.9.16: o BUG ANNMAP-97 geneToExonProbeset threw an error when as.vector=TRUE Changes in version 0.9.15: o NEW ANNMAP-94 Added annmapAddConnection method for setting up databases. Changes in version 0.9.14: o NEW ANNMAP-90 Added generateBridgeData method for helping with BAM file imports. o IMPROVED ANNMAP-93 Refactored out some NCBI->Ensembl seqname mapping functions. o IMPROVED ANNMAP-84 Added ngsBridgePlot examples to the cookbook. Changes in version 0.9.13: o IMPROVED ANNMAP-78 Cookbook now appears when vignette( package='annmap' ) is called. Changes in version 0.9.12: o IMPROVED ANNMAP-74, ANNMAP-75, ANNMAP-76; Fixed warnings and notes when using R-2.15 Changes in version 0.9.11: o IMPROVED ANNMAP-73 Methods generalisedNameToNCBI, generalisedNameToEnsembl, seqnameMapping, seqnamesToNCBI and seqnamesToEnsembl added to allow easy renaming of the seqnames column of GRanges data. Changes in version 0.9.10: o IMPROVED ANNMAP-71 Bug in geneToSymbol fixed Changes in version 0.9.9: o IMPROVED ANNMAP-63 We now use GenomicRanges instead of IRanges Changes in version 0.9.8: o IMPROVED ANNMAP-58 Added 4 pos translation documentation to cookbook o BUG ANNMAP-60 Webservice tests were failing o BUG ANNMAP-54 geneToExonProbeset didn't support as.vector Changes in version 0.9.7: o BUG ANNMAP-48 Error in proteinCoordsToGenome in annmap o BUG ANNMAP-47 annmapGenePlot fails to show individual transcripts o IMPROVED ANNMAP-45 Added a NEWS.Rd file to inst Changes in version 0.9.6: o BUG Fixed ANNMAP-44; genomicPlot crashes when called with very small overlapped areas Changes in version 0.9.5: o IMPROVED ANNMAP-41; All InRange methods are now S3 methods which work with character, data.frame or RangedData (see ?annmap.range). o IMPROVED ANNMAP-42; genomicPlot highlights 'colour' column is now 'col' as with all other methods. o BUG ANNMAP-40; genomicPlot crashes if highlights data.frame has unexpected columns.