fishpond

DOI: 10.18129/B9.bioc.fishpond    

Fishpond: downstream methods and tools for expression data

Bioconductor version: Release (3.15)

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>

Installation

To install this package, start R (version "4.2") 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	1. Swish: DE analysis accounting for inferential uncertainty
HTML	R Script	2. SEESAW - Allelic expression analysis with Salmon and Swish
PDF		Reference Manual
Text		NEWS

Details

biocViews	AlternativeSplicing, BatchEffect, DifferentialExpression, DifferentialSplicing, GeneExpression, MultipleComparison, Normalization, RNASeq, Regression, Sequencing, SingleCell, Software, Transcription, Visualization
Version	2.2.0
In Bioconductor since	BioC 3.9 (R-3.6) (3.5 years)
License	GPL-2
Depends
Imports	graphics, stats, utils, methods, abind, gtools, qvalue, S4Vectors, IRanges, SummarizedExperiment, GenomicRanges, matrixStats, svMisc, Rcpp, Matrix, SingleCellExperiment, jsonlite
LinkingTo	Rcpp
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
SystemRequirements	C++11
Enhances
URL	https://github.com/mikelove/fishpond
Depends On Me
Imports Me	singleCellTK
Suggests Me	tximeta, tximport
Links To Me
Build Report

Package Archives

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

Source Package	fishpond_2.2.0.tar.gz
Windows Binary	fishpond_2.2.0.zip
macOS Binary (x86_64)	fishpond_2.2.0.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