ballgown

ballgown performs differential expression analysis of RNA-seq data at transcript, exon, intron, and gene levels using linear modeling of transcript abundance estimates.

Key Features:

• Multi-Level Expression Analysis: Supports differential expression analysis at transcript, exon, intron, and gene resolution.
• Linear Modeling Framework: Applies linear models to continuous abundance measurements such as FPKM values and coverage-derived metrics.
• Integration with Transcriptome Assemblies: Imports transcriptome assemblies in GTF format generated by tools such as Cufflinks or StringTie.
• Quantification Data Support: Uses expression estimates produced by Tablemaker, including transcript-level FPKM values, mapped read counts, and mean per-base coverage.
• Complex Experimental Design Analysis: Supports modeling of continuous covariates, time-course experiments, eQTL studies, and confounded experimental designs.

Scientific Applications:

• RNA-seq Differential Expression Studies: Identifies transcripts, genes, exons, or introns with significant expression changes across experimental conditions.
• Transcript Isoform Expression Analysis: Evaluates isoform-level expression using continuous abundance estimates rather than count-based methods.
• Functional Genomics and eQTL Analysis: Supports statistical modeling of transcript abundance in studies of genetic regulation and temporal gene expression dynamics.

Methodology:

ballgown imports transcriptome assemblies in GTF format and expression estimates generated by Tablemaker or related quantification tools, organizes them into an R/Bioconductor object, and applies linear modeling to abundance metrics such as FPKM and coverage to test for differential expression across experimental conditions.