Fishpond: downstream methods and tools for expression data

This package provides statistical methods and other tools for working with Salmon and Alevin quantification of RNA-seq data. Fishpond contains the Swish non-parametric method for detecting differential transcript expression (DTE). Swish can also be used to detect differential gene expresion (DGE), to perform allelic analysis, or to assess changes in isoform proportions.

Details

The main Swish 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

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

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