NEWS

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FRASER 2.6.1

• Internal: use moved makeTxDbFromGFF function from txdbmaker instead from GenomicFeatures.

FRASER 2.4.6

• Fixing a bug in the annotation, where we miss the annotation for junction, where we do not have any splice site available at the time of annotation. Thanks to @AtaJadidAhari

FRASER 2.4.5

• We fixed a bug affecting unstranded paired-end data. We were counting read fragments instead of read pairs. The counted split reads with the fixed method are, on average, lower by around 20%. If you have such data, please rerun your entire analysis from the start (make sure you have recount=TRUE).

FRASER 2.4.4

• Bugfix: reading fragments instead of read pairs for unstranded paired-end data. If you have such kind of data, please rerun the whole analysis from the start (make sure you have recount=TRUE).

FRASER 2.4.3

• Fix bug in cache

FRASER 2.4.2

• Add Optimal Hard Thresholding to determine optimal encoding dimension #69
• Add singular value plot for optimal encoding dimension
• Add updateSeqlevelsStyle to change seqlevels without internet connection

FRASER 1.99.4

• Bugfix for strand specificity of samples in counting

FRASER 1.99.3

• Bugfix for contig names containing certain characters
• Update of the plot functions to support coloring aberrant status based on p values computed on subsets of genes
• Major update to FRASER2:
• Introduction of new & more robust splice metric Intron Jaccard Index
• Only Intron Jaccard Index metric used by default
• Improved gene level pvalue calculation and internal storage
• Introduction of option to limit FDR correction to user-defined subsets of genes per sample (e.g. OMIM genes with rare variant)
• Updated internal pseudocount parameter and default delta Jaccard cutoff
• Junction filtering adapted to usage of Intron Jaccard Index metric
• Require min expression of N >= 10 in 25% of the samples
• Results table:
• Functionality to flag outliers in blacklist regions of the genome
• Functionality to annotate the predicted type of aberrantSplicing (e.g. exon skipping, intron retention etc.)
• Several updates in the plotting functions
• introduction of manhattan plot functionality
• possibility to create sashimi plots to visualize read coverage in the bam files for outliers

FRASER 1.8.1

• Bugfix in merging splicing counts (#41)

FRASER 1.6.1

• Fixing quantile filtering defaults (#28)
• Require min expression in 5% instead of 95% of the samples
• Require min expression on both sides of the junction
• Align FRASER package with DROP pipeline (#24)
• Move temp directory from tempdir() to working directory getwd() (#35)
• Improve visualizations and Improve documentation
• Improve internal object validation
• Minor bugfixes (eg. #37)

FRASER 1.2.1

• Add merging of external counts
• Add publication
• Minor bugfixes

FRASER 1.1.6

• Use proper S3/S4 methods to share functions between packages
• Minor API changes due to S3/S4 changes (e.g fds -> object)
• Switch from psiSite to theta
• Improved documentation
• Minor bugfixes

FRASER 1.1.3

• Update and adjust injectOutlier and hyperParameter functions
• Option to compute z scores in logit space or not
• Add cap value [0.01,0.99] to logit function
• Use pairedEnd counting with Rsubread
• Correct assayName pajd -> padj
• Minor bugfixes

FRASER 1.1.2

• Option to consider only the standard chromosomes in the counting
• Option to include additional columns from mcols(fds) in the result table
• 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
• Minor bugfixes

FRASER 1.1.1

• Bugfix correcting the strand specific counting for paired-end reads

FRASER 0.99.1

• Introduction of the shinyApp

FRASER 0.99.0

• This is the initial setup of the FRASER package.
• Use SummarizedExperiment as superclass
• Integrate package into the Bioconductor infrastructure