CHANGES IN VERSION 1.0.5 ------------------------ NEW FEATURES o gtf2gr transcript_id and gene_id attribute names can now be customized. BUG FIXES o annotatePeaks returned an error when remove_unmatched was disabled. o Increased filter accuracy of annotatePeaks when min_genelength > 0. CHANGES IN VERSION 1.0.4 ------------------------ NEW FEATURES o Setting psize to 'preserve' will enable macs2gr to return the original peak lengths. o annotatePeaks can now preserve the gene_id column if present. o Added an option to gtf2gr which defines the GTF feature type entry to be filtered during parsing CHANGES IN VERSION 1.0.3 ------------------------ BUG FIXES o Improved type checking. CHANGES IN VERSION 1.0.2 ------------------------ BUG FIXES o Fixed a bug which resulted in wrong quality score cut off in parseReads(). o annotatePeaks() did not accept input gtf files with present values CHANGES IN VERSION 1.0.1 ------------------------ BUG FIXES o Fixed a bug which resulted in wrong density maps of overlapping regions from sliceN. CHANGES IN VERSION 1.0.0 ------------------------ NEW FEATURES o Release version with several minor, mainly manual related improvements. CHANGES IN VERSION 0.99.3 ------------------------ NEW FEATURES o Renamed all C files. Registering now takes place in a separate file. o plotTV can now alternatively take a character vector of IDs matching 'transcript_id' in the gtf instead of a GRanges object. This is useful to plot RNA-Seq data matching without regions. BUG FIXES o Added PACKAGE argument to .call o readthrough_pairs argument to parseReads declared experimental. o Removed the matching RNA-Seq data set and added pasillaBamSubset as an example for RNA-Seq visualisation. CHANGES IN VERSION 0.99.2 ------------------------ NEW FEATURES o Added getter methods for all slots of DensityContainer and inherited classes for individual access. Added setter methods for spliced and ex_name o removed dc.size() and added the slot 'size' instead. Also added env and data_pointer slots to class DensityContainer o improved documentation of S4 methods with usage section o gtf2df and macs2df renamed to gtf2gr and macs2gr respectively. They are now returning a GRanges object. o annotatePeaks takes and returns only GRanges objects. o id2tss renamed to peak2tss and now returning an updated GRanges object o plotTV accepts GRanges objects rather than data.frames for gtf and peaks input BUG FIXES o Removed all direct slot accessions o Removed unnecessary call to dyn.load and dyn.unload in parseReads() CHANGES IN VERSION 0.99.1 ------------------------ NEW FEATURES o plotTV returns ordering to reproduce kmeans clustering BUG FIXES o sliceNT did not flip the exons on the negative strand o Argument rowv to plotTV did not work with expression threshold remove_lowex o Installation on 32bit Windows was not possible