fishpond
Fishpond: downstream methods and tools for expression data
Bioconductor version: 3.23 · Package version: 2.18.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("fishpond")Details
| Maintainer | Michael Love <michaelisaiahlove@gmail.com> |
| 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] |
| License | GPL-2 |
| URL | https://thelovelab.github.io/fishpond, https://thelovelab.com/mikelove/fishpond |
| Bug Reports | https://support.bioconductor.org/tag/fishpond |
| Downloads rank | 824 |
| Source branch | RELEASE_3_23 |
| biocViews | AlternativeSplicing, BatchEffect, DifferentialExpression, DifferentialSplicing, GeneExpression, MultipleComparison, Normalization, RNASeq, Regression, Sequencing, SingleCell, Software, Transcription, Visualization |
Documentation
- Swish: differential expression accounting for inferential uncertainty
- SEESAW - Allelic expression analysis with Salmon and Swish
Download
Dependencies
Imports: graphics, stats, utils, methods, abind, gtools, qvalue, S4Vectors, IRanges, SummarizedExperiment, GenomicRanges, matrixStats, svMisc, Matrix, SingleCellExperiment, jsonlite
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