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:

- `scaleInfReps` - scaling transcript or gene expression data

- `labelKeep` - labelling which features have sufficient counts

- `swish` - perform non-parametric differential analysis

- Plots, e.g., `plotMASwish`, `plotInfReps`

- `isoformProportions` - convert counts to isoform proportions

- `makeInfReps` - create pseudo-inferential replicates

- `splitSwish` - split Swish analysis across jobs with Snakemake

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 contributor code of conduct:

https://github.com/mikelove/fishpond

### Author(s)

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

### References

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. https://doi.org/10.1093/nar/gkz622

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. https://doi.org/10.1101/2020.07.06.189639

[Package fishpond version 1.6.0 Index]