fishpond

fishpond implements differential transcript and gene expression analysis of RNA-seq data using inferential replicates for uncertainty of abundance quantification, as generated by Gibbs sampling or bootstrap sampling.

Key Features:

• Inferential Replicate Analysis: Methods utilize inferential replicates from Gibbs sampling or bootstrap sampling to account for uncertainty in abundance quantification.
• Salmon Quantification Utilities: Functions for working with Salmon quantification files.
• Alevin Quantification Utilities: Functions for working with Alevin quantification files.

Scientific Applications:

• Differential Transcript Expression: Statistical analysis of differential transcript expression using inferential replicates.
• Differential Gene Expression: Statistical analysis of differential gene expression using inferential replicates.

Methodology:

The package uses inferential replicates generated by Gibbs sampling or bootstrap sampling to model uncertainty of abundance quantification in RNA-seq data analysis.