DOI: 10.18129/B9.bioc.fishpond  

Fishpond: downstream methods and tools for expression data

Bioconductor version: Release (3.17)

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>

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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


biocViews AlternativeSplicing, BatchEffect, DifferentialExpression, DifferentialSplicing, GeneExpression, MultipleComparison, Normalization, RNASeq, Regression, Sequencing, SingleCell, Software, Transcription, Visualization
Version 2.6.2
In Bioconductor since BioC 3.9 (R-3.6) (4.5 years)
License GPL-2
Imports graphics, stats, utils, methods, abind, gtools, qvalue, S4Vectors, IRanges, SummarizedExperiment, GenomicRanges, matrixStats, svMisc, Matrix, SingleCellExperiment, jsonlite
Suggests testthat, knitr, rmarkdown, macrophage, tximeta,, samr, DESeq2, apeglm, tximportData, limma, ensembldb, EnsDb.Hsapiens.v86, GenomicFeatures, AnnotationDbi, pheatmap, Gviz, GenomeInfoDb, data.table
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