rnalib

rnalib provides a Python framework for creating custom transcriptomics analysis methods and stepwise annotation of gene features with local and remote genomics datasets.

Key Features:

• Random access support: Built on pysam and pyBigWig to enable efficient access to relevant subregions of large, genome-wide datasets.
• Extended filtering and access capabilities: Expands upon the filtering and access capabilities of pysam and pyBigWig with additional checks to prevent common errors when integrating genomics datasets.
• Transcriptome class: An object-oriented class providing methods for stepwise annotation of gene features with both local and remote data sources.
• API design: Cleanly separates immutable genomic locations from associated, mutable data, and offers methods for iterating, querying, and exporting collated datasets.
• Gene feature annotation: Supports annotation of diverse gene features including transcript isoforms, introns, and untranslated regions.

Scientific Applications:

• Transcriptomics data analysis: Development of novel transcriptomics data analysis tools and methods through a fast, readable, reproducible, and robust framework.
• Genomics data integration: Association of gene features with relevant subsections of large genomics datasets across diverse data formats.
• Genomic location-based querying: Efficient querying of genomics data based on genomic locations and annotation attributes.

Methodology:

rnalib is built on existing Python libraries pysam and pyBigWig, with an object-oriented Transcriptome class that separates immutable genomic locations from mutable associated data.