NEWS

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BUSpaRse 1.5.2 (2020-12-04)

• Updated code that queries Ensembl for new version of biomaRt.
• Make sure there're no NAs in tr2g_intron when chrs_only = TRUE.
• Bypassed issue in BSgenome::getSeq in get_velocity_files when genome is DNAStringSet.

BUSpaRse 1.1.4 (2020-04-23)

• Now tr2g_* functions can also extract transcriptomes.
• By default, tr2g_* functions write the tr2g.tsv to disk.
• Write filtered GTF and GFF3 files.
• List of available gene and transcript biotypes from Ensembl can be queried by data().
• RefSeq GFF3 annotations can now be used in tr2g_gff3.

BUSpaRse 1.1.3 (2020-04-06)

• Allow filtering gene and transcript biotypes in tr2g and get_velocity_files
• Allow removing scaffolds and haplotypes from genome annotations for tr2g

BUSpaRse 1.1.2 (2020-02-06)

• Removed RcppParallel and data.table dependencies, and hence all C++ multithreading
• Added knee_plot function
• Changed default in read_count_output to tcc = FALSE

BUSpaRse 1.1.1 (2020-01-29)

• Sort GRanges for RNA velocity to make sure that exons are in the right order; split no longer sorts within each element of GRangesList.
• Export subset_annot, which makes sure that all chromosomes in the annotation are present in the genome prior to transcriptome extraction.

BUSpaRse 0.99.25 (2019-09-11)

• Added message to indicate when get_velocity_files is extracting exon-exon junctions.
• Restored "separate" to be default isoform_action in get_velocity_files.

BUSpaRse 0.99.24 (2019-09-06)

• When sorting tr2g from file, now the file must be formatted in ways required by bustools.

BUSpaRse 0.99.23 (2019-09-06)

• Previous two version bumps did not accompany changes; those were used to trigger rebuilds on Bioconductor.
• Added the functionality to use L-1 (L is read length) bases around exon-exon junction to better distinguish between spliced and unspliced transcripts for RNA velocity.
• Fixed serious problem with get_velocity_file that counted reads mapping to exons of length between L-1 and 2(L-1) as from unspliced transcript. This was done by an reimplementation of the method to get flanked intronic ranges.
• Changed default isoform_action to "collapse".
• Make sure that all transcripts in tr2g.tsv from get_velocity_files are in the transcriptome.

BUSpaRse 0.99.20 (2019-08-26)

• Addressed Bioconductor review.

BUSpaRse 0.99.19 (2019-07-23)

• Finished get_velocity_files to generate files required for kallisto | bustools RNA velocity.

BUSpaRse 0.99.0 (2019-06-21)

• Submitted package to Bioconductor for review