CHANGES IN VERSION 1.6.4 ------------------------- o Made the plotDispLSD function visible (now proporly exported) CHANGES IN VERSION 1.6.3 ------------------------- o Added a plotDispLSD function that adds a density estimate color map to the DESeq plotDispEsts function. CHANGES IN VERSION 1.6.2 ------------------------- o Released the constraint on the gtf annotation file parsing to allow for gtf file without the "exon_number" attribute such as those retrieved from UCSC. CHANGES IN VERSION 1.6.1 ------------------------- o Adapted the package dependency o Added a check to stop processing whenever annotation are outside of the chromosomes. CHANGES IN VERSION 1.6.0 ------------------------- o No changes, Bioconductor release version 2.12 CHANGES IN VERSION 1.5.1 ------------------------- o Adapted the dependencies version to match the Bioconductor release version 2.11 BUG FIXES o corrected an innapropriate function call to an internal function (as in stable version 1.4.2) CHANGES IN VERSION 1.5.0 ------------------------- o No changes, Bioconductor development version 2.12 CHANGES IN VERSION 1.4.2 ------------------------- BUG FIXES o corrected an innapropriate function call to an internal function CHANGES IN VERSION 1.4.1 ------------------------- o Adapted the dependencies version to match the Bioconductor release version 2.11 CHANGES IN VERSION 1.4.0 ------------------------- o No changes, Bioconductor release version 2.11 CHANGES IN VERSION 1.3.14 ------------------------- NEW FEATURES o easyRNASeq now returns a SummarizedExperiment in an effort to consolidate the objects used for Next Generation Sequencing in Bioconductor. This is the new default of the count function. The count function is a new function to supersed easyRNASeq in the coming development version (1.5.x) to consolidate the parameters and output of the easyRNASeq function. BUG FIXES o corrected a validity check that went permissive. o changed the print method to display the read length range when dealing with variable read lengths rather than every single value. CHANGES IN VERSION 1.3.13 ------------------------- BUG FIXES o Same correction as in the stable version 1.2.5, but for those already corrected in version 1.3.3. CHANGES IN VERSION 1.3.12 ------------------------- o Providing the 'outputFormat' argument is not necessary anymore, it defaults to matrix (i.e. count table). o Relaxed the gtf file checking. If the gene_name is absent, the gene_id is used instead. o Improved some reporting and remove a bottle-neck occuring when there are many sequences in the reference. BUG FIXES o Ensure that only the matched ranges are returned when reading gapped alignments. o The library size is more exactly calculated and is the number of aligned reads. o Corrected a bug in the validity checking that prevented bam files created by different aligners using the same reference to be processed as the reference sequences were not ordered in the same fashion. CHANGES IN VERSION 1.3.11 ------------------------- BUG FIXES o Fixed a bug in the gtf file handling reported by Mark Robinson. CHANGES IN VERSION 1.3.10 ------------------------- o Some vignette discrepancies have been corrected. Thanks to Richard Friedman for spotting them. o Providing the 'filesDirectory' argument is not necessary anymore, if the files to proceed are present in the current directory. Indeed, this parameter now defaults to the current directory as can be found out using 'getwd()'. BUG FIXES o Fixed a bug introduced by a change in the IRanges coverage function return value. CHANGES IN VERSION 1.3.9 ------------------------- o Added the manuscript citation. o Updated the package version dependencies. BUG FIXES o Improved the support for reads of different lengths. o A cosmetic change to report read lengths as well when read files with variable read length are processed. o Corrected a bug and enhanced the loading of gtf annotation files. Thanks to Tomasz Kulinski for spotting the issue and providing the dataset to reproduce it. CHANGES IN VERSION 1.3.8 ------------------------- NEW FEATURES o Now bam files can be processed in parallel (long time request from Wade Davis). If the easyRNASeq argument 'nbCore' is greater than 1 (1 being the default), then that many core will be used to process the read files in parallel. Pay attention not to use too many cores and have enough memory available. The memory load scales up linearly with the number of files processed. CHANGES IN VERSION 1.3.7 ------------------------- NEW FEATURES o easyRNASeq now supports read of different lenghts. Thanks to Mark Robinson for the toy dataset. o Added a function that lists existing organism conversion when applying the validity checks. o Added a bp.coverage to the fetchCoverage function that defaults to FALSE. To allow for variable length reads, it now returns read coverage proportion per bp by default. o Added additional checks in the .checkArguments internal function. BUG FIXES o Not a real bug, but more a consolidation. When an organism is unknown and no custom.map is provided, then the validity checks are turned off and a warning is emitted. o Providing the chr.sizes as as list has been deprecated. Only named numeric vector are supported. o Removed a now useless warning in the .readGffGtf function. o Modified the RPKM function generic to avoid using a 'protected' word as argument: i.e. 'unique' was replaced by 'simplify' CHANGES IN VERSION 1.3.6 ------------------------- NEW FEATURES o It is now possible to pass arguments to list files through the three dots. I.e. setting recursive=TRUE is now possible. BUG FIXES o Corrected a bug in the .getArguments internal function. CHANGES IN VERSION 1.3.5 ------------------------- NEW FEATURES o bam is now the default format for the easyRNASeq method. o chromosome sizes are now extracted from the BAM header when the 'chr.sizes' argument is set to "auto". Thanks to Simon Anders for pushing that off my TODO list and the nice implementation. BUG FIXES o Adapted to an API change of the edgeR package for estimating the tagwise dispersion. CHANGES IN VERSION 1.3.4 ------------------------- NEW FEATURES o Added an additional validity check for chromosome names Thanks to Simon Anders for generating a reproducible use-case for that. Same change as in the stable version 1.2.3 o Ensure that gtf with non Ensembl ID are correctly parsed as well. CHANGES IN VERSION 1.3.3 ------------------------- o Converted the package to use Roxygen2, a Doxygen like in-source documentation system for generating the RD and NAMESPACE. The original man page were converted using the Rd2roxygen package and the resulting in-source documentation manually edited. NEW FEATURES o Added a type accessor for Genome_intervals object o Added a coercion to GRangesList from Genome_intervals object BUG FIXES o Adapted to the new arguments of the edgeR estimateTagwiseDisp function o Removed the dispersion.method argument from the plotMeanVar edgeR method call as this argument is defunct. CHANGES IN VERSION 1.3.2 ------------------------- BUG FIXES o Corrected a bug that was considering a GTF file as a GFF file. Thanks to Simon Anders for spotting this. CHANGES IN VERSION 1.3.1 ------------------------- NEW FEATURES o Added an enhanced read length check (same as stable 1.2.1 change) CHANGES IN VERSION 1.3.0 ------------------------- o New development version for Bioconductor 2.11 CHANGES IN VERSION 1.2.5 ------------------------- BUG FIXES o Corrected a bug in the condition file name checking. o When using edgeR, it was not possible to de-activate the drawing of the quality assessment plots. o Some edgeR changes to the API have been ported to the stable R version, should not have occured... The following are changes that adapt to that new API, changes ported from version the easyRNASeq development version 1.3.3... o Adapted to the new arguments of the edgeR estimateTagwiseDisp function o Removed the dispersion.method argument from the plotMeanVar edgeR method call as this argument is defunct. CHANGES IN VERSION 1.2.4 ------------------------- o Added the manuscript citation. o Updated the package version dependencies. CHANGES IN VERSION 1.2.3 ------------------------- NEW FEATURES o Added an additional validity check for chromosome names Thanks to Simon Anders for generating a reproducible use-case for that. o Ensure that gtf with non Ensembl ID are correctly parsed as well. CHANGES IN VERSION 1.2.2 ------------------------- BUG FIXES o Corrected a bug that was considering a GTF file as a GFF file. Thanks to Simon Anders for spotting this. CHANGES IN VERSION 1.2.1 ------------------------- NEW FEATURES o Added an enhanced read length check CHANGES IN VERSION 1.2.0 ------------------------- o Stable version released as part of Bioconductor 2.10 CHANGES IN VERSION 1.1.10 ------------------------- NEW FEATURES o Added a naPositionFilter extending ShortRead srFilters BUG FIXES o Worked on Wade Davis case with 3 different sets of chromosome names in the three different input (reads, annotation, chromosome sizes) o Worked on smoother error handling when not using bam files. Again through Wade Davis example o Ensured that chromosome names conversion occurs whether provided with a factor or a character vector o extended the NAMESPACE CHANGES IN VERSION 1.1.9 ------------------------ BUG FIXES o Added an \alias{RNAseq} to ease the class documentation access; an H.Pages suggestion o Changed the DESCRIPTION file to make sure that the latest ShortRead (1.13.13) and BiocGenerics (0.1.11) package are required CHANGES IN VERSION 1.1.8 ------------------------ BUG FIXES o Corrected the last occurence of the deprecated matchMatrix call o Corrected an issue on windows raised by the parallel package. Thanks to Wade Davis for pointing that one out. CHANGES IN VERSION 1.1.7 ------------------------ BUG FIXES o Fixed the NAMESPACE and the vignette generation CHANGES IN VERSION 1.1.6 ------------------------ BUG FIXES o Thanks to Francesco Lescai, a bug was fixed. Namely I was not expecting the chromosome names in the bam files and in the chromosome name lists to be two different set with a common intersect. I always consider that one would be the subset of the other one. Now, when such situation occurs only the common set is kept and used for the calculations. o Herve Pages changed the findOverlaps value. It is now an object of the Hits class that does not support the matchMatrix accessor anymore. The code was adapted to the new accessor queryHits. o Corrected the package structure to add a vignettes sub-directory. Moved the relevant files there CHANGES IN VERSION 1.1.5 ------------------------ BUG FIXES o Removed the fitInfo method extension to the DESeq package as it as been implemented in that package o Reworked the plotDispersionEstimates and .normalizationDispatcher function to deal with the new fitInfo function (the information is stored in an environment rather than in a list) CHANGES IN VERSION 1.1.4 ------------------------ o Package introduced in Bioconductor