# Fishpond: downstream methods and tools for expression data

## Documentation for package ‘fishpond’ version 2.4.0

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

## Help Pages

fishpond-package | Fishpond: downstream methods and tools for expression data
addStatsFromCSV | Read statistics and nulls from CSV file
alevinEC | Construct a sparse matrix of transcript compatibility counts from alevin output
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
makeInfReps | Make pseudo-inferential replicates from mean and variance
makeSimSwishData | Make simulated data for swish for examples/testing
makeTx2Tss | Make a GRanges linking transcripts to TSS within gene
miniSwish | Helper function for distributing Swish on a subset of data
plotAllelicGene | Plot allelic counts in a gene context using Gviz
plotAllelicHeatmap | Plot allelic ratio heatmap
plotInfReps | Plot inferential replicates for a gene or transcript
plotMASwish | MA plot - log fold change over average counts
salmonEC | Construct a sparse matrix of transcript compatibility counts from salmon output
scaleInfReps | Scale inferential replicate counts
splitSwish | Function for splitting SummarizedExperiment into separate RDS files
swish | Swish method: differential expression accounting for inferential uncertainty