Fishpond: differential transcript and gene expression with inferential replicates

Documentation for package ‘fishpond’ version 1.8.0

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
isoformProportions	Create isoform proportions from scaled data
labelKeep	Label rows to keep based on minimal count
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