fishpond-package: Downstream methods for Salmon and Alevin expression data

Description Details Author(s) References


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).


The main functions are:

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

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


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


Swish method:

Zhu, A., Srivastava, A., Ibrahim, J.G., Patro, R., Love, M.I. (2019) Nonparametric expression analysis using inferential replicate counts. Nucleic Acids Research.

Compression, makeInfReps and splitSwish:

Van Buren, S., Sarkar, H., Srivastava, A., Rashid, N.U., Patro, R., Love, M.I. (2020) Compression of quantification uncertainty for scRNA-seq counts. bioRxiv.

fishpond documentation built on Nov. 8, 2020, 7:54 p.m.