Changes in version 0.99.0 (2021-04-15)
+ Submitted to Bioconductor
Changes in version 1.3.4 (2022-10-26)
+ Added a multi-sample single-cell pipeline (sc_long_multisample_pipeline)
+ Individual steps are exported as functions
+ Added a plotting function (sc_annotate)
+ Added support for using bambu for isoform discovery
Changes in version 1.8.0 (2023-10-2)
+ Updated find_barcode to use flexiplex and cutadapt
+ Added blaze for demultiplexing without known barcodes
+ Added gene quantification
Changes in version 2.0.0 (2024-10-29)
+ Added coverage visualization (plot_coverage)
+ Added find_variant
+ Reimplement sc_mutations with Rcpp
+ Added Oarfish as a quantification option
+ Added plot_demultiplex for visualizing find_barcode results
Changes in version 2.3.1 (2025-05-22)
+ Refactored pipelines to S4 classes
+ Included minimap2, oarfish binaries
+ Added a permutation based DTU method in sc_DTU_analysis
Changes in version 2.3.3 (2025-06-18)
+ Gzipped FASTQ outputs to reduce file size
+ Support adding minimap2 indexed genome (as `genome_mmi`)
+ Added crew controllers support, steps can now be submitted to slurm etc.