Isosceles 0.2.0

Isosceles 0.2.0 release

Changes since Isosceles release 0.03:

• 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.)

Isosceles 0.1.0

Isosceles 0.1.0 release

Isosceles 0.0.3

Isosceles release for the review process

Isosceles 0.0.2

Isosceles release for the review process

Isosceles 0.0.1

Isosceles release for the review process