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.
Packaged: 2021-02-21 21:50:00 UTC; evanbiederstedt

org.Mm.eg.db, pcaMethods, pheatmap, rgl, rmarkdown, robustbase,
Packaged: 2022-04-19 21:15:59 UTC; evanbiederstedt

Packaged: 2021-03-03 23:47:36 UTC; evanbiederstedt

Packaged: 2021-05-03 19:03:01 UTC; evanbiederstedt

Packaged: 2021-06-28 21:10:26 UTC; evanbiederstedt

Packaged: 2021-08-11 19:29:40 UTC; evanbiederstedt

Packaged: 2021-10-06 20:04:33 UTC; evanbiederstedt

Packaged: 2021-11-15 01:41:10 UTC; evanbiederstedt

Packaged: 2021-12-12 09:33:22 UTC; evanbiederstedt

Packaged: 2022-03-02 19:53:50 UTC; evanbiederstedt

Title: Analyze Bacterial Pangenomes in R with 'Pagoo'
Description: Provides an encapsulated, object-oriented class system for
analyzing bacterial pangenomes. For a definition of this concept, see
package as backend. It was designed in order to facilitate and speed-up
the comparative analysis of multiple bacterial genomes, standardizing and
optimizing routine tasks performed everyday. There are a handful of things
done everyday when working with bacterial pangenomes: subset, summarize,
extract, visualize and store data. So, 'pagoo' is intended to facilitate these
tasks as much as possible. For a description of the implemented data structure
person("Ignacio", "Ferres", , "iferres@pasteur.edu.uy", role =  c("aut", "cre"),
person("Gregorio", "Iraola", , "iferres@pasteur.edu.uy", role = c("aut"),
person("Institut Pasteur de Montevideo", role = c("fnd")
Depends: R (>= 3.5.0), S4Vectors, Biostrings, ggplot2
Imports: R6, reshape2, vegan, GenomicRanges, BiocGenerics,
shinyWidgets, shinydashboard, DT, plotly, magrittr, heatmaply,
Suggests: micropan, patchwork, ape, phangorn, pegas, DECIPHER,
rhierbaps, IRanges, knitr, rmarkdown, testthat, covr
Author: Ignacio Ferres [aut, cre] (<https://orcid.org/0000-0003-0910-6568>),