fishpond

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see fishpond.

Fishpond: differential transcript and gene expression with inferential replicates


Bioconductor version: 3.14

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: Anzi 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], Scott Van Buren [ctb], Dongze He [ctb], Steve Lianoglou [ctb], Wes Wilson [ctb]

Maintainer: Michael Love <michaelisaiahlove at gmail.com>

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

Installation

To install this package, start R (version "4.1") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("fishpond")

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

Documentation

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

browseVignettes("fishpond")
DTE and DGE with inferential replicates HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews AlternativeSplicing, BatchEffect, DifferentialExpression, DifferentialSplicing, GeneExpression, MultipleComparison, Normalization, RNASeq, Regression, Sequencing, SingleCell, Software, Transcription, Visualization
Version 2.0.1
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License GPL-2
Depends
Imports graphics, stats, utils, methods, abind, gtools, qvalue, S4Vectors, SummarizedExperiment, matrixStats, svMisc, Rcpp, Matrix, SingleCellExperiment, jsonlite
System Requirements C++11
URL https://github.com/mikelove/fishpond
See More
Suggests testthat, knitr, rmarkdown, macrophage, tximeta, org.Hs.eg.db, samr, DESeq2, apeglm, tximportData, limma
Linking To Rcpp
Enhances
Depends On Me
Imports Me singleCellTK
Suggests Me tximport
Links To Me
Build Report Build Report

Package Archives

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

Source Package fishpond_2.0.1.tar.gz
Windows Binary fishpond_2.0.1.zip
macOS 10.13 (High Sierra) fishpond_2.0.1.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/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.14 Source Archive