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

In fishpond: Fishpond: differential transcript and gene expression with inferential replicates

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

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