DOI: 10.18129/B9.bioc.fishpond    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see fishpond.

Fishpond: differential transcript and gene expression with inferential replicates

Bioconductor version: 3.11

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 utilities for working with Salmon and Alevin quantification files.

Author: Anqi Zhu, Avi Srivastava, Joseph Ibrahim, Rob Patro, Michael Love

Maintainer: Michael Love <michaelisaiahlove at>

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


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HTML R Script DTE and DGE with inferential replicates
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biocViews AlternativeSplicing, BatchEffect, DifferentialExpression, DifferentialSplicing, GeneExpression, MultipleComparison, Normalization, RNASeq, Regression, Sequencing, SingleCell, Software, Transcription, Visualization
Version 1.4.1
In Bioconductor since BioC 3.9 (R-3.6) (1.5 years)
License GPL-2
Imports graphics, stats, utils, methods, abind, gtools, qvalue, S4Vectors, SummarizedExperiment, matrixStats, svMisc, Rcpp, Matrix
LinkingTo Rcpp
Suggests testthat, knitr, rmarkdown, macrophage, tximeta,, samr, DESeq2, apeglm
SystemRequirements C++11
Depends On Me
Imports Me
Suggests Me tximport
Links To Me
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