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Fishpond: downstream methods and tools for expression data

Bioconductor version: Release (3.18)

Fishpond contains methods for differential transcript and gene expression analysis of RNA-seq data using inferential replicates for uncertainty of abundance quantification, as generated by Gibbs sampling or bootstrap sampling. Also the package contains a number of utilities for working with Salmon and Alevin quantification files.

Author: Anqi Zhu [aut, ctb], Michael Love [aut, cre], Avi Srivastava [aut, ctb], Rob Patro [aut, ctb], Joseph Ibrahim [aut, ctb], Hirak Sarkar [ctb], Euphy Wu [ctb], Noor Pratap Singh [ctb], Scott Van Buren [ctb], Dongze He [ctb], Steve Lianoglou [ctb], Wes Wilson [ctb], Jeroen Gilis [ctb]

Maintainer: Michael Love <michaelisaiahlove at gmail.com>

Citation (from within R, enter citation("fishpond")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

1. Swish: DE analysis accounting for inferential uncertainty HTML R Script
2. SEESAW - Allelic expression analysis with Salmon and Swish HTML R Script
Reference Manual PDF


biocViews AlternativeSplicing, BatchEffect, DifferentialExpression, DifferentialSplicing, GeneExpression, MultipleComparison, Normalization, RNASeq, Regression, Sequencing, SingleCell, Software, Transcription, Visualization
Version 2.8.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License GPL-2
Imports graphics, stats, utils, methods, abind, gtools, qvalue, S4Vectors, IRanges, SummarizedExperiment, GenomicRanges, matrixStats, svMisc, Matrix, SingleCellExperiment, jsonlite
System Requirements
URL https://thelovelab.github.io/fishpond https://thelovelab.com/mikelove/fishpond
Bug Reports https://support.bioconductor.org/tag/fishpond
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Suggests testthat, knitr, rmarkdown, macrophage, tximeta, org.Hs.eg.db, samr, DESeq2, apeglm, tximportData, limma, ensembldb, EnsDb.Hsapiens.v86, GenomicFeatures, AnnotationDbi, pheatmap, Gviz, GenomeInfoDb, data.table
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package fishpond_2.8.0.tar.gz
Windows Binary fishpond_2.8.0.zip (64-bit only)
macOS Binary (x86_64) fishpond_2.8.0.tgz
macOS Binary (arm64) fishpond_2.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/fishpond
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/fishpond
Bioc Package Browser https://code.bioconductor.org/browse/fishpond/
Package Short Url https://bioconductor.org/packages/fishpond/
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