HTSeq 2.0 provides a more extensive application programming interface including a new representation for sparse genomic data, enhancements for htseq-count to suit single-cell omics, a new script for data using cell and molecular barcodes, improved documentation, testing and deployment, bug fixes and Python 3 support.
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Putri, G. H., Anders, S., Pyl, P. T., Pimanda, J. E., & Zanini, F. (2022). Analysing high-throughput sequencing data in Python with HTSeq 2.0. Bioinformatics, 38(10), 2943–2945. https://doi.org/10.1093/bioinformatics/btac166