tximport

"tximport" is an R package to enhance the analysis of RNA-seq data by facilitating the integration of transcript-level abundance estimates into gene-level analyses, which are often more interpretable and statistically robust. This software addresses a critical step in transcriptomic studies: quantifying abundance levels of genes or transcripts from high-throughput RNA-seq data. While various methods exist for quantifying these features, ranging from simple read counting to complex estimation procedures, "tximport" focuses on improving the reliability and interpretability of gene-level differential expression analysis.

The developers of "tximport" provide a key insight into the advantage of gene-level abundance estimates over transcript-level analyses, both in performance and ease of interpretation. They highlight a significant challenge in RNA-seq data analysis: differential isoform usage can lead to inflated false discovery rates in differential gene expression analysis when based on simple count matrices. The package addresses this issue by utilizing offsets derived from transcript-level abundance estimates, thereby mitigating the potential for false positive findings in gene-level comparisons.