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fishpond

Fishpond: downstream methods and tools for expression data

Bioconductor version: Release (3.17)

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 a number of utilities for working with Salmon and Alevin quantification files.

Author: Anqi 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], Noor Pratap Singh [ctb], Scott Van Buren [ctb], Dongze He [ctb], Steve Lianoglou [ctb], Wes Wilson [ctb], Jeroen Gilis [ctb]

Maintainer: Michael Love <michaelisaiahlove at gmail.com>

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

Installation

To install this package, start R (version "4.3") 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")
1. Swish: DE analysis accounting for inferential uncertainty HTML R Script
2. SEESAW - Allelic expression analysis with Salmon and Swish 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 2.6.2
In Bioconductor since BioC 3.9 (R-3.6) (4.5 years)
License GPL-2
Depends
Imports graphics, stats, utils, methods, abind, gtools, qvalue, S4Vectors, IRanges, SummarizedExperiment, GenomicRanges, matrixStats, svMisc, Matrix, SingleCellExperiment, jsonlite
Linking To
Suggests testthat, knitr, rmarkdown, macrophage, tximeta, org.Hs.eg.db, samr, DESeq2, apeglm, tximportData, limma, ensembldb, EnsDb.Hsapiens.v86, GenomicFeatures, AnnotationDbi, pheatmap, Gviz, GenomeInfoDb, data.table
System Requirements
Enhances
URL https://mikelove.github.io/fishpond https://github.com/mikelove/fishpond
Bug Reports https://support.bioconductor.org/tag/fishpond
See More
Depends On Me
Imports Me
Suggests Me tximeta
Links To Me
Build Report  

Package Archives

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

Source Package fishpond_2.6.2.tar.gz
Windows Binary fishpond_2.6.2.zip
macOS Binary (x86_64) fishpond_2.6.2.tgz
macOS Binary (arm64) fishpond_2.6.2.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 3.17 Source Archive