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
fishpond-package        Fishpond: downstream methods and tools for
                        expression data
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
