fishpond
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see fishpond.
Fishpond: differential transcript and gene expression with inferential replicates
Bioconductor version: 3.9
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.
Author: Anqi Zhu, Avi Srivastava, Joseph Ibrahim, Rob Patro, Michael Love
Maintainer: Michael Love <michaelisaiahlove at gmail.com>
citation("fishpond")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text |
Details
| biocViews | AlternativeSplicing, BatchEffect, DifferentialExpression, DifferentialSplicing, GeneExpression, MultipleComparison, Normalization, RNASeq, Regression, Sequencing, SingleCell, Software, Transcription, Visualization |
| Version | 1.0.2 |
| 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 |
| System Requirements | |
| URL | https://github.com/mikelove/fishpond |
See More
| Suggests | testthat, knitr, rmarkdown, macrophage, tximeta, org.Hs.eg.db, samr, DESeq2, apeglm |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | fishpond_1.0.2.tar.gz |
| Windows Binary | fishpond_1.0.2.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | fishpond_1.0.2.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 3.9 | Source Archive |