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>

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

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 10.13 (High Sierra) 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

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