Package: pagoda2
Title: Single Cell Analysis and Differential Expression
Version: 1.0.15
Authors@R: c(person("Nikolas","Barkas", email="nikolas_barkas@hms.harvard.edu", role="aut"), person("Viktor", "Petukhov", email="viktor.s.petuhov@ya.ru", role="aut"), person("Peter", "Kharchenko", email = "peter_kharchenko@hms.harvard.edu", role = "aut"), person("Simon", "Steiger", email = "simon.steiger@gmail.com", role = "ctb"), person("Rasmus", "Rydbirk", email = "rrydbirk@bmb.sdu.dk", role = "ctb"), person("Evan", "Biederstedt", email="evan.biederstedt@gmail.com", role=c("cre", "aut")))
Description: Analyzing and interactively exploring large-scale
        single-cell RNA-seq datasets. 'pagoda2' primarily performs
        normalization and differential gene expression analysis, with
        an interactive application for exploring single-cell RNA-seq
        datasets. It performs basic tasks such as cell size
        normalization, gene variance normalization, and can be used to
        identify subpopulations and run differential expression within
        individual samples. 'pagoda2' was written to rapidly process
        modern large-scale scRNAseq datasets of approximately 1e6
        cells. The companion web application allows users to explore
        which gene expression patterns form the different
        subpopulations within your data. The package also serves as the
        primary method for preprocessing data for conos,
        <https://github.com/kharchenkolab/conos>. This package
        interacts with data available through the 'p2data' package,
        which is available in a 'drat' repository. To access this data
        package, see the instructions at
        <https://github.com/kharchenkolab/pagoda2>. The size of the
        'p2data' package is approximately 6 MB.
License: GPL-3
Copyright: See the file COPYRIGHTS for various pagoda2 copyright
        details
Encoding: UTF-8
Depends: R (>= 3.5.0), Matrix, igraph
biocViews:
Imports: dendsort, drat, fastcluster, graphics, grDevices, irlba,
        magrittr, MASS, mgcv, methods, N2R, parallel, plyr, R.utils,
        Rcpp, rjson, rlang, R6, RMTstat, Rook, Rtsne, sccore (>=
        0.1.1), stats, urltools, utils
RoxygenNote: 7.3.2
Suggests: AnnotationDbi, base64enc, BiocGenerics, BiocParallel,
        colorRamps, data.table, dbscan, dplyr, ggplot2, GO.db,
        gridExtra, KernSmooth, knitr, org.Dr.eg.db, org.Hs.eg.db,
        org.Mm.eg.db, pcaMethods, pheatmap, rgl, rmarkdown, robustbase,
        scde, testthat, uwot
URL: https://github.com/kharchenkolab/pagoda2
BugReports: https://github.com/kharchenkolab/pagoda2/issues
NeedsCompilation: yes
LinkingTo: Rcpp, RcppArmadillo, RcppProgress, RcppEigen
Author: Nikolas Barkas [aut], Viktor Petukhov [aut], Peter Kharchenko
        [aut], Simon Steiger [ctb], Rasmus Rydbirk [ctb], Evan
        Biederstedt [cre, aut]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>
Config/pak/sysreqs: libglpk-dev libxml2-dev
Repository: https://kharchenkolab.r-universe.dev
Date/Publication: 2026-04-01 17:53:53 UTC
RemoteUrl: https://github.com/kharchenkolab/pagoda2
RemoteRef: HEAD
RemoteSha: 35f71aba4349354c77a8beb208796dbfd5df616b
Packaged: 2026-06-24 05:15:02 UTC; root