fishpond

DOI: 10.18129/B9.bioc.fishpond    

This is the development version of fishpond; to use it, please install the devel version of Bioconductor.

Fishpond: differential transcript and gene expression with inferential replicates

Bioconductor version: Development (3.10)

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 gmail.com>

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

Installation

To install this package, start R (version "3.6") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.1.24
In Bioconductor since BioC 3.9 (R-3.6) (< 6 months)
License GPL-2
Depends
Imports graphics, stats, utils, methods, abind, gtools, qvalue, S4Vectors, SummarizedExperiment, matrixStats, svMisc, Rcpp
LinkingTo Rcpp
Suggests testthat, knitr, rmarkdown, macrophage, tximeta, org.Hs.eg.db, samr, DESeq2, apeglm
SystemRequirements C++11
Enhances
URL https://github.com/mikelove/fishpond
Depends On Me
Imports Me
Suggests Me tximport
Links To Me
Build Report  

Package Archives

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

Source Package fishpond_1.1.24.tar.gz
Windows Binary fishpond_1.1.24.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) fishpond_1.1.24.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

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