Changes in version 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. Changes in version 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. Changes in version 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 Changes in version 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 Changes in version 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. Changes in version 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. Changes in version 0.99.24 (2019-09-06) - When sorting tr2g from file, now the file must be formatted in ways required by bustools. Changes in version 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. Changes in version 0.99.20 (2019-08-26) - Addressed Bioconductor review. Changes in version 0.99.19 (2019-07-23) - Finished get_velocity_files to generate files required for kallisto | bustools RNA velocity. Changes in version 0.99.0 (2019-06-21) - Submitted package to Bioconductor for review