NEWS

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FLAMES 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.

FLAMES 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

FLAMES 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

FLAMES 1.8.0

• Updated find_barcode to use flexiplex and cutadapt
• Added blaze for demultiplexing without known barcodes
• Added gene quantification

FLAMES 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

FLAMES 0.99.0 (2021-04-15)

• Submitted to Bioconductor