pytximport

pytximport: Transcript-to-Gene Quantification Import and Summarization

pytximport imports transcript quantification outputs from Salmon, Kallisto, and RSEM and summarizes transcript-level estimates to gene-level counts for downstream gene expression analysis.

Key Features:

• Versatile Input Support: Parses transcript quantification files generated by Salmon, Kallisto, and RSEM.
• Bias Correction Modes: Implements multiple bias correction modes to adjust transcript count estimates.
• Inferential Replicates Handling: Processes inferential replicates for statistical analysis of gene expression.
• Gene-Level Summarization: Aggregates transcript-level counts to gene-level expression matrices.
• Transcript-Level Export and Mapping: Exports transcript-level data and generates transcript-to-gene mapping tables.
• Biotype Filtering: Filters transcripts by annotated biotype prior to summarization.

Scientific Applications:

• Differential Gene Expression Analysis: Generates gene-level count matrices from RNA-seq transcript quantification files for downstream statistical testing.
• RNA-seq Workflow Integration: Integrates transcript quantification and gene-level summarization within Python-based transcriptomic analysis pipelines.

Methodology:

Implements a Python adaptation of the tximport R package framework to import transcript abundance estimates, apply bias correction, incorporate inferential replicates, and compute gene-level summaries from RNA-seq quantification outputs.