Fishpond: differential transcript and gene expression with inferential replicates

Documentation for package ‘fishpond’ version 1.3.16

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