Givanna H Putri1,2, Simon Anders3, Paul Theodor Pyl4, John E Pimanda1,2,5,6, Fabio Zanini1,2,7. 1. Prince of Wales Clinical School, University of New South Wales, Sydney, Australia NSW. 2. Adult Cancer Program, Lowy Cancer Research Centre, University of New South Wales, Sydney, Australia NSW. 3. Bioquant Center, University of Heidelberg, 69120 Heidelberg, Germany. 4. Division of Surgery, Oncology and Pathology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden. 5. Department of Pathology, School of Medical Sciences, University of New South Wales, Sydney, 2052, Australia NSW. 6. Department of Haematology, the Prince of Wales Hospital, Sydney, Australia NSW. 7. Cellular Genomics Futures Institute, University of New South Wales, Sydney, Australia NSW.
Abstract
SUMMARY: HTSeq 2.0 provides a more extensive API including a new representation for sparse genomic data, enhancements in 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. AVAILABILITY AND IMPLEMENTATION: HTSeq 2.0 is released as an open-source software under the GNU General Public License and available from the Python Package Index at https://pypi.python.org/pypi/HTSeq. The source code is available on Github at https://github.com/htseq/htseq. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
SUMMARY: HTSeq 2.0 provides a more extensive API including a new representation for sparse genomic data, enhancements in 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. AVAILABILITY AND IMPLEMENTATION: HTSeq 2.0 is released as an open-source software under the GNU General Public License and available from the Python Package Index at https://pypi.python.org/pypi/HTSeq. The source code is available on Github at https://github.com/htseq/htseq. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Steve Huhn; Meiping Chang; Amit Kumar; Ren Liu; Bo Jiang; Michael Betenbaugh; Henry Lin; Gregg Nyberg; Zhimei Du Journal: iScience Date: 2022-03-14