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DESCRIPTION
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DESCRIPTION
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Package: fishpond
Title: Fishpond: differential transcript and gene expression
with inferential replicates
Version: 1.7.0
Authors@R: c(
person("Anzi", "Zhu", role = c("aut","ctb")),
person("Michael", "Love", email="[email protected]", role = c("aut","cre")),
person("Avi", "Srivastava", role = c("aut","ctb")),
person("Rob", "Patro", role = c("aut","ctb")),
person("Joseph", "Ibrahim", role = c("aut","ctb")),
person("Hirak", "Sarkar", role = "ctb"),
person("Scott", "Van Buren", role = "ctb")
)
Maintainer: Michael Love <[email protected]>
Description: 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 utilities for working with Salmon and Alevin
quantification files.
Imports:
graphics, stats, utils, methods, abind, gtools, qvalue, S4Vectors,
SummarizedExperiment, matrixStats, svMisc, Rcpp, Matrix
Suggests: testthat, knitr, rmarkdown, macrophage, tximeta, org.Hs.eg.db,
samr, DESeq2, apeglm, tximportData, SingleCellExperiment
LinkingTo: Rcpp
SystemRequirements: C++11
License: GPL-2
Encoding: UTF-8
URL: https://github.com/mikelove/fishpond
biocViews: Sequencing, RNASeq, GeneExpression,
Transcription, Normalization, Regression,
MultipleComparison, BatchEffect, Visualization,
DifferentialExpression, DifferentialSplicing,
AlternativeSplicing, SingleCell
VignetteBuilder: knitr
LazyData: true
RoxygenNote: 7.1.0