fishpond
Fishpond: downstream methods and tools for expression data
Bioconductor version: Release (3.20)
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("fishpond")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | AlternativeSplicing, BatchEffect, DifferentialExpression, DifferentialSplicing, GeneExpression, MultipleComparison, Normalization, RNASeq, Regression, Sequencing, SingleCell, Software, Transcription, Visualization |
| Version | 2.12.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5.5 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.
| Source Package | fishpond_2.12.0.tar.gz |
| Windows Binary (x86_64) | fishpond_2.12.0.zip |
| macOS Binary (x86_64) | fishpond_2.12.0.tgz |
| macOS Binary (arm64) | fishpond_2.12.0.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 |