# Fishpond: differential transcript and gene expression with inferential replicates

## Documentation for package ‘fishpond’ version 2.0.0

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

## Help Pages

fishpond-package | Downstream methods for Salmon and Alevin expression data
addStatsFromCSV | Read statistics and nulls from CSV file
computeInfRV | Compute inferential relative variance (InfRV)
deswish | deswish: DESeq2-apeglm With Inferential Samples Helps
getTrace | Obtain a trace of inferential replicates for a sample
importAllelicCounts | Import allelic counts as a SummarizedExperiment
isoformProportions | Create isoform proportions from scaled data
labelKeep | Label rows to keep based on minimal count
loadFry | Load in data from alevin-fry USA mode
load_fry_raw | Load in data from alevin-fry USA mode
makeInfReps | Make pseudo-inferential replicates from mean and variance
makeSimSwishData | Make simulated data for swish for examples/testing
miniSwish | Helper function for distributing Swish on a subset of data
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
splitSwish | Function for splitting SummarizedExperiment into separate RDS files
swish | swish: SAMseq With Inferential Samples Helps