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Isosceles 0.2.0

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@mkabza mkabza released this 09 Apr 02:05
· 12 commits to devel since this release
0.2.0
68ebfc6

Isosceles 0.2.0 release

Changes since Isosceles release 0.0.3:

  • Regarding GitHub issue #2
    • Parsing BAM files has been made more stringent by disallowing secondary alignments, as well as reads that are duplicated or don't pass QC criteria
    • Inter-chromosomal alignments are now automatically removed from the analysis
    • Added new assertion to the prepare_transcripts function, which should catch problems with non-unique intron_positions values in input data
    • Updated the unit tests to reflect the introduced changes
  • Regarding GitHub issue #5
    • Added a section on preparing single-cell data to the main vignette
  • Regarding GitHub issue #6
    • Added the filter_psi_events function for filtering PSI events suitable to be used with downstream DEXSeq analysis
  • Changes affecting transcript detection sensitivity and FDR
    • Set the default value of the rescue_annotated_introns argument of the prepare_transcripts function to TRUE, ensuring that introns found in genome annotations are taken into account even if they don't have known intron motifs
    • Added the max_intron_length argument for the maximum allowed intron length (default 5e6) to the prepare_transcripts function
  • Preparing input data for DEXSeq analysis
    • Removed the tcc_to_dexseq function and replaced it with a more flexible approach using new add_psi_counts and psi_to_dexseq functions
    • Updated the mouse E18 brain data analysis vignette to describe the new way of preparing input data for DEXSeq analysis
  • SIRV data analysis
    • Updated the prepare_reference_annotations function to work with malformed GTF files (e.g. genes having transcripts on different strands or transcripts having different strand than their exons) and give warnings regarding encountered problems
    • Updated the assign_intron_strand function to assign unknown strand to introns having known intron motifs on both strands
  • Added the gtf_to_intron_bed function for preparing intron BED files suitable for read alignment using minimap2
  • Added the plot_splicing_support_levels function for plotting spliced read counts by splicing support level
  • Updated the prepare_transcripts function to allow users to use longer transcript stable hash identifier in case of a hashing collision error
  • Updated the merge_annotated_genes function to replace functions deprecated in igraph package version 2.0.0 with their newer equivalents
  • Updated default argument values for various functions (e.g. the default run mode of the bam_to_tcc function) to make them consistent with settings used in benchmarks from the paper
  • Updated the main vignette to include information about recommended flags for minimap2, newly added functions, computation parallelization strategies used by Isosceles and suggested settings for SIRV data analysis
  • Updated Isosceles installation instructions (in README.md and the main vignette) to include solutions for common problems with dependency versions
  • Updated the required versions of dependencies in the DESCRIPTION file to deal with package installation problems
  • Fixed typos and other minor errors in the vignettes and unit tests
  • Updated the README.md file (added information about testing the package, included links to the publication preprint and Isosceles Singularity image etc.)
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