Package: fishpond
Title: Fishpond: differential transcript and gene expression with
        inferential replicates
Version: 1.4.1
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,
        Matrix
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: 7.1.0
git_url: https://git.bioconductor.org/packages/fishpond
git_branch: RELEASE_3_11
git_last_commit: 08f430c
git_last_commit_date: 2020-05-12
Date/Publication: 2020-05-12
NeedsCompilation: yes
Packaged: 2020-05-13 06:34:32 UTC; biocbuild
Built: R 4.0.0; i386-w64-mingw32; 2020-05-13 17:47:01 UTC; windows
Archs: i386, x64
