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license: GPL-3.0-only
title: 'pagoda2: Single Cell Analysis and Differential Expression'
version: 1.0.12
doi: 10.32614/CRAN.package.pagoda2
abstract: 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.
authors:
- family-names: Barkas
  given-names: Nikolas
  email: nikolas_barkas@hms.harvard.edu
- family-names: Petukhov
  given-names: Viktor
  email: viktor.s.petuhov@ya.ru
- family-names: Kharchenko
  given-names: Peter
  email: peter_kharchenko@hms.harvard.edu
- family-names: Biederstedt
  given-names: Evan
  email: evan.biederstedt@gmail.com
repository: https://CRAN.R-project.org/package=pagoda2
repository-code: https://github.com/kharchenkolab/pagoda2
url: https://github.com/kharchenkolab/pagoda2
date-released: '2024-02-27'
contact:
- family-names: Biederstedt
  given-names: Evan
  email: evan.biederstedt@gmail.com