fishpond

DOI: 10.18129/B9.bioc.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>

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")

 

HTML	R Script	DTE and DGE with inferential replicates
PDF		Reference Manual
Text		NEWS

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) (3 years)
License	GPL-2
Depends
Imports	graphics, stats, utils, methods, abind, gtools, qvalue, S4Vectors, SummarizedExperiment, matrixStats, svMisc, Rcpp, Matrix, SingleCellExperiment, jsonlite
LinkingTo	Rcpp
Suggests	testthat, knitr, rmarkdown, macrophage, tximeta, org.Hs.eg.db, samr, DESeq2, apeglm, tximportData, limma
SystemRequirements	C++11
Enhances
URL	https://github.com/mikelove/fishpond
Depends On Me
Imports Me	singleCellTK
Suggests Me	tximport
Links To Me
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
Package Short Url	https://bioconductor.org/packages/fishpond/
Package Downloads Report	Download Stats