tximport

tximport integrates transcript-level abundance estimates into gene-level RNA-seq analysis workflows within R/Bioconductor.

Key Features:

• Integration with quantification pipelines: Imports transcript-level estimated counts and transcript lengths from common quantification pipelines.
• Summarization capability: Summarizes transcript-level information into gene-level count and abundance matrices compatible with downstream gene-level analysis tools.
• Offsets for statistical adjustment: Computes offsets from transcript-level data to mitigate biases and potential inflated false discovery rates caused by differential isoform usage.

Scientific Applications:

• Gene-level abundance estimation: Supports conversion of transcript-level abundance estimates into gene-level measures for comparative transcriptomic analyses.
• Differential expression inference: Provides offsets to improve statistical inference in differential gene expression analyses, especially when differential isoform usage occurs.
• Comparative RNA-seq studies: Facilitates comparisons of abundance levels or transcriptomic composition across conditions using RNA-seq data.

Methodology:

Summarizes transcript-level estimated counts and transcript lengths into gene-level matrices and computes offsets from transcript-level abundance estimates to account for differential isoform usage.