Package: fishpond
Title: Fishpond: differential transcript and gene expression with
        inferential replicates
Version: 1.3.4
Author: Anqi Zhu, Avi Srivastava, Joseph Ibrahim, Rob Patro, Michael Love
Maintainer: Michael Love <michaelisaiahlove@gmail.com>
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
Suggests: testthat, knitr, rmarkdown, macrophage, tximeta,
        org.Hs.eg.db, samr, DESeq2, apeglm
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: 7.0.2
git_url: https://git.bioconductor.org/packages/fishpond
git_branch: master
git_last_commit: 9ab75f5
git_last_commit_date: 2020-01-02
Date/Publication: 2020-01-02
NeedsCompilation: yes
Packaged: 2020-01-03 05:24:32 UTC; biocbuild
Built: R 4.0.0; x86_64-apple-darwin15.6.0; 2020-01-03 15:07:14 UTC; unix
