FRASER/NEWS at master · gagneurlab/FRASER · GitHub

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CHANGES IN VERSION 2.6.1
-------------------------
    o Internal: use moved makeTxDbFromGFF function from txdbmaker instead from GenomicFeatures.

    CHANGES IN VERSION 2.4.6
-------------------------
    o 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

CHANGES IN VERSION 2.4.5
-------------------------
    o 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).

CHANGES IN VERSION 2.4.4
-------------------------
    o 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).

CHANGES IN VERSION 2.4.3
-------------------------
    o Fix bug in cache

CHANGES IN VERSION 2.4.2
-------------------------
    o Add Optimal Hard Thresholding to determine optimal encoding dimension #69
    o Add singular value plot for optimal encoding dimension
    o Add updateSeqlevelsStyle to change seqlevels without internet connection

CHANGES IN VERSION 1.99.4
-------------------------
    o Bugfix for strand specificity of samples in counting

CHANGES IN VERSION 1.99.3
-------------------------
    o Bugfix for contig names containing certain characters
    o Update of the plot functions to support coloring 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