fishpond-package {fishpond}R Documentation

Downstream methods for Salmon and Alevin expression data

Description

This package provides statistical methods and other tools for working with Salmon and Alevin quantification of RNA-seq data. In particular, it contains the Swish non-parametric method for detecting differential transcript expression (DTE). Swish can also be used to detect differential gene expresion (DGE).

Details

The main functions are:

All software-related questions should be posted to the Bioconductor Support Site:

https://support.bioconductor.org

The code can be viewed at the GitHub repository, which also lists the contributtor code of conduct:

https://github.com/mikelove/fishpond

Author(s)

Anqi Zhu, Avi Srivastava, Joseph G. Ibrahim, Rob Patro, Michael I. Love

References

Zhu, A., Srivastava, A., Ibrahim, J.G., Patro, R., Love, M.I. (2019) Nonparametric expression analysis using inferential replicate counts. Nucleic Acids Research. https://doi.org/10.1093/nar/gkz622


[Package fishpond version 1.4.1 Index]