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NEWS
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NEWS
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CHANGES IN VERSION 1.99.3
-------------------------
o Bugfix for contig names containing certain characters
CHANGES IN VERSION 1.99.2
-------------------------
o Update of the plot functions to support colorring aberrant status based
on p values computed on subsets of genes
-------------------------
o Major update to FRASER2:
o Introduction of new & more robust splice metric Intron Jaccard Index
o Only Intron Jaccard Index metric used by default
o Improved gene level pvalue calculation and internal storage
o Introduction of option to limit FDR correction to user-defined
subsets of genes per sample (e.g. OMIM genes with rare variant)
o Updated internal pseudocount parameter and default delta Jaccard
cutoff
o Junction filtering adapted to usage of Intron Jaccard Index metric
o Require min expression of N >= 10 in 25% of the samples
o Results table:
o Functionality to flag outliers in blacklist regions of the genome
o Functionality to annotate the predicted type of aberrantSplicing
(e.g. exon skipping, intron retention etc.)
o Several updates in the plotting functions
o introduction of manhattan plot functionality
o possibility to create sashimi plots to visualize read coverage in
the bam files for outliers
CHANGES IN VERSION 1.8.1
-------------------------
o Bugfix in merging splicing counts (#41)
CHANGES IN VERSION 1.6.1
-------------------------
o Fixing quantile filtering defaults (#28)
o Require min expression in 5% instead of 95% of the samples
o Require min expression on both sides of the junction
o Align FRASER package with DROP pipeline (#24)
o Move temp directory from tempdir() to working directory getwd() (#35)
o Improve visualizations and Improve documentation
o Improve internal object validation
o Minor bugfixes (eg. #37)
CHANGES IN VERSION 1.2.1
o Add merging of external counts
o Add publication
o Minor bugfixes
CHANGES IN VERSION 1.1.6
-------------------------
o Use proper S3/S4 methods to share functions between packages
o Minor API changes due to S3/S4 changes (e.g fds -> object)
o Switch from psiSite to theta
o Improved documentation
o Minor bugfixes
CHANGES IN VERSION 1.1.3
-------------------------
o Update and adjust injectOutlier and hyperParameter functions
o Option to compute z scores in logit space or not
o Add cap value [0.01,0.99] to logit function
o Use pairedEnd counting with Rsubread
o Correct assayName pajd -> padj
o Minor bugfixes
CHANGES IN VERSION 1.1.2
-------------------------
o Option to consider only the standard chromosomes in the counting
o Option to include additional columns from mcols(fds) in the result table
o Annotation of junctions with corresponding gene names/ids now produces
an additional column in mcols(fds) that contains further gene names/ids
if the junction overlaps with multiple genes
o Minor bugfixes
CHANGES IN VERSION 1.1.1
-------------------------
o Bugfix correcting the strand specific counting for paired-end reads
CHANGES IN VERSION 0.99.1
-------------------------
o Introduction of the shinyApp
CHANGES IN VERSION 0.99.0
-------------------------
o This is the initial setup of the FRASER package.
o Use SummarizedExperiment as superclass
o Integrate package into the Bioconductor infrastructure