Fishpond: downstream methods and tools for expression data

Documentation for package ‘fishpond’ version 2.10.0

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