h4HTSeq

h4HTSeq performs programmatic analysis of high-throughput sequencing (HTS) data, providing gene expression quantification and sparse genomic-data representations for single-cell omics and related genomic studies.

Key Features:

• Extensive API: Provides an enriched Python API that includes a novel representation for sparse genomic data to improve efficiency and memory usage.
• Enhancements to htseq-count: Optimizes htseq-count for single-cell omics to enable more accurate and efficient quantification of gene expression levels from sequencing data.
• Support for cell and molecular barcodes: Includes a dedicated script for processing cell and molecular barcodes used in single-cell RNA sequencing (scRNA-seq) experiments.
• Sparse genomic data structures: Employs sparse genomic data structures to optimize performance and scalability for large datasets.
• Bug fixes and Python 3 support: Addresses prior issues through bug fixes and ensures compatibility with Python 3.

Scientific Applications:

• Single-cell omics and scRNA-seq: Enables gene expression quantification and barcode processing for studies of cellular heterogeneity and cell-level gene expression.
• High-throughput sequencing gene expression analysis: Supports programmatic analysis and quantification workflows for HTS experiments at the gene level.

Methodology:

Implements a Python API with a novel representation and sparse genomic data structures, includes enhancements to htseq-count for gene-level quantification, and provides a script for processing cell and molecular barcodes; supports Python 3.