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("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 | ||
| 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 |