IMPROVED Version number changed to reflect Bioconductor repository
IMPROVED ANNMAP-121 The data is now cached in a dedicated directory instead of in the home directory
IMPROVED ANNMAP-121 URLs for the project and the download location for the database was updated
IMPROVED ANNMAP-121 Allow setting of WS base url for local testing
IMPROVED ANNMAP-119 as.vector=TRUE results are now named
IMPROVED ANNMAP-120 genomeToTranscriptCoords could handle coding regions
BUG Check for uniqueness in transcriptToCodingExon, transcriptToCodingRange, transcriptToUtrExon and transcriptToUtrRange
NEW Added transcriptToUtrExon
IMPROVED Sequence removed from transcriptToCodingExon
IMPROVED ANNMAP-115 Added method geneToGeneRegionTrack to generate a list of Gviz GeneRegionTrack elements that can be passed to plotTracks
BUG ANNMAP-118 transcriptToCodingRange( ..., end='3' ) returns whole transcript for untranslated transcripts.
IMPROVED ANNMAP-114 Added additional logging when using webservice
IMPROVED ANNMAP-116 Introduce function(s) to calculate the coding length of a gene(s) – See: ?nonIntronicGeneLength and ?nonIntronicTranscriptLength.
IMPROVED ANNMAP-114 Added additional logging when using webservice
IMPROVED ANNMAP-113 Added documentation to cookbook for webservice
IMPROVED webservice json to data.frame speed improvements
BUG ANNMAP-112 transcriptCoordsToGenome and proteinCoordsToGenome both failed when returning a GRanges object as I had strand as a numeric, rather than an integer.
IMPROVED genomicPlot when passed a .genes data.frame used to call geneDetails on it to ensure the data was in the correct format. This has been removed, so that you can pass custom regions in and have them plotted on the graph.
BUG ANNMAP-110 XXXInRange( NULL ) used to throw an error. It now returns NULL.
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.
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.
BUG ANNMAP-101 ngsBridgePlot called with no genes in range had a huge border.
BUG ANNMAP-106 Empty ngsBridgePlot trace should draw line at 0.
BUG ANNMAP-107 transcriptToCodingRange was very slow.
NEW Initial Release to Bioconductor
BUG ANNMAP-98 A call to transcriptToTranslatedprobes for transcripts in HPRT1 caused a crash
BUG ANNMAP-97 geneToExonProbeset threw an error when as.vector=TRUE
NEW ANNMAP-94 Added annmapAddConnection method for setting up databases.
NEW ANNMAP-90 Added generateBridgeData method for helping with BAM file imports.
IMPROVED ANNMAP-93 Refactored out some NCBI->Ensembl seqname mapping functions.
IMPROVED ANNMAP-84 Added ngsBridgePlot examples to the cookbook.
IMPROVED ANNMAP-78 Cookbook now appears when vignette( package='annmap' ) is called.
IMPROVED ANNMAP-74, ANNMAP-75, ANNMAP-76; Fixed warnings and notes when using R-2.15
IMPROVED ANNMAP-73 Methods generalisedNameToNCBI, generalisedNameToEnsembl, seqnameMapping, seqnamesToNCBI and seqnamesToEnsembl added to allow easy renaming of the seqnames column of GRanges data.
IMPROVED ANNMAP-71 Bug in geneToSymbol fixed
IMPROVED ANNMAP-63 We now use GenomicRanges instead of IRanges
IMPROVED ANNMAP-58 Added 4 pos translation documentation to cookbook
BUG ANNMAP-60 Webservice tests were failing
BUG ANNMAP-54 geneToExonProbeset didn't support as.vector
BUG ANNMAP-48 Error in proteinCoordsToGenome in annmap
BUG ANNMAP-47 annmapGenePlot fails to show individual transcripts
IMPROVED ANNMAP-45 Added a NEWS.Rd file to inst
BUG Fixed ANNMAP-44; genomicPlot crashes when called with very small overlapped areas
IMPROVED ANNMAP-41; All InRange methods are now S3 methods which work with character, data.frame or RangedData (see ?annmap.range).
IMPROVED ANNMAP-42; genomicPlot highlights 'colour' column is now 'col' as with all other methods.
BUG ANNMAP-40; genomicPlot crashes if highlights data.frame has unexpected columns.