Reference

Fishpond

fishpond-package

Fishpond: downstream methods and tools for expression data

Swish method

scaleInfReps()

Scale inferential replicate counts

labelKeep()

Label rows to keep based on minimal count

swish()

Swish method: differential expression accounting for inferential uncertainty

Main Swish plotting functions

plotInfReps()

Plot inferential replicates for a gene or transcript

plotMASwish()

MA plot - log fold change over average counts

Helper functions

computeInfRV()

Compute inferential relative variance (InfRV)

getTrace()

Obtain a trace of inferential replicates for a sample

isoformProportions()

Create isoform proportions from scaled data

makeSimSwishData()

Make simulated data for swish for examples/testing

Import and utilities

loadFry()

Load in data from alevin-fry USA mode

alevinEC()

Construct a sparse matrix of transcript compatibility counts from alevin output

salmonEC()

Construct a sparse matrix of transcript compatibility counts from salmon output

Allelic analysis and plotting

importAllelicCounts()

Import allelic counts as a SummarizedExperiment

makeTx2Tss()

Make a GRanges linking transcripts to TSS within gene

plotAllelicGene()

Plot allelic counts in a gene context using Gviz

plotAllelicHeatmap()

Plot allelic ratio heatmap

Compression

splitSwish()

Function for splitting SummarizedExperiment into separate RDS files

addStatsFromCSV()

Read statistics and nulls from CSV file

makeInfReps()

Make pseudo-inferential replicates from mean and variance

miniSwish()

Helper function for distributing Swish on a subset of data

Experimental

deswish()

deswish: DESeq2-apeglm With Inferential Samples Helps