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Bioconductor - fishpond

fishpond

This is the released version of fishpond; for the devel version, see fishpond.

Fishpond: downstream methods and tools for expression data

Bioconductor version: Release (3.21)

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 "4.5") 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 2.14.0 In Bioconductor since BioC 3.9 (R-3.6) (6 years) License GPL-2 Depends Imports graphics, stats, utils, methods, abind, gtools, qvalue, S4Vectors, IRanges, SummarizedExperiment, GenomicRanges, matrixStats, svMisc, Matrix, SingleCellExperiment, jsonlite System Requirements URL https://thelovelab.github.io/fishpond https://thelovelab.com/mikelove/fishpond Bug Reports https://support.bioconductor.org/tag/fishpond See More 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 Linking To Enhances Depends On Me Imports Me Suggests Me tximeta Links To Me Build Report Build Report Package Archives

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

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