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# fishpond <img id="fishpond_logo" src="man/figures/fishpond.png" align="right" width="125"/> [![R build status](]( ## Fishpond: downstream methods and tools for expression data Fishpond contains a method, `swish()`, for differential transcript and gene expression analysis of RNA-seq data using inferential replicates. Also the package contains utilities for working with *Salmon*, *alevin*, and *alevin-fry* quantification data, including `loadFry()`. ## Quick start The following paradigm is used for running a Swish analysis: ``` y <- tximeta(coldata) # reads in counts and inf reps y <- scaleInfReps(y) # scales counts y <- labelKeep(y) # labels features to keep set.seed(1) # for reproducibility y <- swish(y, x="condition") # simplest Swish case ``` ## How does Swish work Swish accounts for inferential uncertainty in expression estimates by averaging test statistics over a number of *inferential replicate* datasets, either posterior samples or bootstrap samples. This is inspired by a method called [SAMseq](, hence we named our method *Swish*, for "SAMseq With Inferential Samples Helps". Averaging over inferential replicates produces a different test statistic than what one would obtain using only point estimates for expression level. For example, one of the tests possible with `swish()` is a correlation test of expression level over a condition variable. We can visualize the distribution of inferential replicates with `plotInfReps()`: ![](man/figures/plotInfReps.png) The test statistic is formed by averaging over these sets of data: ![](man/figures/swish.gif) p-values and q-values are computed through permutation of samples (see vignette for details on permutation schemes). The *Swish* method is described in the following publication: > Zhu, A., Srivastava, A., Ibrahim, J.G., Patro, R., Love, M.I. > "Nonparametric expression analysis using inferential replicate counts" > *Nucleic Acids Research* (2019) 47(18):e105 > [PMC6765120]( The *SEESAW* method for allelic expression analysis is described in the following preprint: > Euphy Wu, Noor P. Singh, Kwangbom Choi, Mohsen Zakeri, Matthew > Vincent, Gary A. Churchill, Cheryl L. Ackert-Bicknell, Rob Patro, > Michael I. Love. > "Detecting isoform-level allelic imbalance accounting for > inferential uncertainty" *bioRxiv* (2022) > [doi: 10.1101/2022.08.12.503785]( ## Installation This package can be installed via Bioconductor: ``` BiocManager::install("fishpond") ``` ## Funding This work was funded by NIH NHGRI R01-HG009937.