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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")
):
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.
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 |
Reference Manual | ||
Text | NEWS |
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 |
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 |
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