Analysing high-throughput sequencing data in Python with HTSeq 2.0

2021/12/02 by Putri, Givanna H, Anders, Simon, Pyl, Paul Theodor +2 · 17 citations
#FOS: Biological sciences #Genomics (q-bio.GN) #Quantitative Methods (q-bio.QM)

paper · doi:10.48550/arxiv.2112.00939

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 Licence 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. Contact: [email protected]

Cited by

• Loss of systemic anti-viral immunity and LMP1-driven suppressive myeloid tumour niches converge to shape the immunobiology of Epstein-Barr virus-positive diffuse large B-cell lymphoma
• ZEB1 drives terminal erythroid maturation by controlling the GATA2–KLF1 regulatory switch
• Comparative Genomic and Transcriptomic Analysis Reveals Why Paenarthrobacter Strains Are Specialists in the Degradation of the Fungicide Iprodione
• Genomic Signatures of Selection Across Climate Gradients and a Geographic Mosaic of Coevolution in an Ant Social Parasite–Host System
• l-2-Hydroxyglutarate impairs neuronal differentiation through epigenetic activation of MYC expression
• AMF primes immune genes against Puccinia hordei (Brown rust) in Hordeum vulgare but does not reduce pathogen burden
• Genetically tractable embryonic cell lines from sea urchins Lytechinus variegatus and Strongylocentrotus purpuratus
• Genetic determinants of monocyte splicing are enriched for disease susceptibility loci
• Phytochrome-mediated light perception in dodders drives haustorium development through epigenetic mechanisms
• Maternal stress triggers early-life eczema through fetal mast cell programming
• Bile Acid Analogs with Anti-Germination Activities for Prophylaxis of Clostridioides difficile Infection Alter Bile Acid Homeostasis in the Enterohepatic Cycle
• Phosphorylation deficient inducible cAMP early repressor (ICER) modulates tumorigenesis and survival in a transgenic zebrafish ( Danio rerio ) model of melanoma
• Mutations Elevate an Underground Pathway to a Physiologically Relevant Protopathway
• Evolution of SL-RNA Genes and Their Splicing Targets in Parasitic Flatworms
• Genomic Patterns of Loss of Distyly and Polyploidization in Primroses
• White-Brown switching controls phenotypic plasticity and virulence of Candida auris
• Bimodal centromeres in pentaploid dogroses shed light on their unique meiosis

Related

• HTSlib: C library for reading/writing high-throughput sequencing data
• Gene count estimation with pytximport enables reproducible analysis of bulk RNA sequencing data in Python
• PyamilySeq: A Python Tool for Interpretable Gene (Re)Clustering and Pangenomic Inference Across Species and Genera
• Contributions of the Petabyte Scale Sequence Search Codeathon toward efforts to scale sequence-based searches on SRA
• Python - All a Scientist Needs