# Fishpond: differential transcript and gene expression with inferential replicates

## Documentation for package ‘fishpond’ version 1.4.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

fishpond-package | Downstream methods for Salmon and Alevin expression data
computeInfRV | Compute inferential relative variance (InfRV)
deswish | deswish: DESeq2-apeglm With Inferential Samples Helps
isoformProportions | Create isoform proportions from scaled data
labelKeep | Label rows to keep based on minimal count
makeSimSwishData | Make simulated data for swish for examples/testing
plotInfReps | Plot inferential replicates for a gene or transcript
plotMASwish | MA plot
readEDS | readEDS - a utility function for quickly reading in Alevin's EDS format
scaleInfReps | Scale inferential replicate counts
swish | swish: SAMseq With Inferential Samples Helps