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pagoda2
View on CRAN: Click
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Download and install pagoda2 package within the R console
Install from CRAN:
install.packages("pagoda2")
Install from Github:
library("remotes")
install_github("cran/pagoda2")
Install by package version:
library("remotes")
install_version("pagoda2", "1.0.12")
Attach the package and use:
library("pagoda2")
Maintained by
Evan Biederstedt
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2021-01-28
Latest Update: 2024-02-27
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, . 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 . The size of the 'p2data' package is approximately 6 MB.
How to cite:
Evan Biederstedt (2021). pagoda2: Single Cell Analysis and Differential Expression. R package version 1.0.12, https://cran.r-project.org/web/packages/pagoda2
Previous versions and publish date:
1.0.0 (2021-01-28 13:30), 1.0.1 (2021-02-23 15:10), 1.0.2 (2021-03-04 08:50), 1.0.3 (2021-05-04 00:00), 1.0.4 (2021-06-29 08:10), 1.0.5 (2021-08-11 21:50), 1.0.6 (2021-10-06 22:40), 1.0.7 (2021-11-15 06:20), 1.0.8 (2021-12-12 11:00), 1.0.9 (2022-03-02 21:40), 1.0.10 (2022-04-19 23:40), 1.0.11 (2023-08-08 21:20)
Other packages that cited pagoda2 R package
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Other R packages that pagoda2 depends,
imports, suggests or enhances
Functions, R codes and Examples using
the pagoda2 R package
Some associated functions: Mode . Pagoda2 . areColors . armaCor . basicP2proc . basicP2web . buildWijMatrix . calcMulticlassified . cellsPerSelectionGroup . cldend2array . collapse.aspect.clusters . compareClusterings . diffExprOnP2FromWebSelection . diffExprOnP2FromWebSelectionOneGroup . dot-onUnload . extendedP2proc . factorFromP2Selection . factorListToMetadata . factorToP2selection . gene.vs.molecule.cell.filter . generateClassificationAnnotation . get.control.geneset . get.de.geneset . getCellsInSelections . getClusterLabelsFromSelection . getColorsFromP2Selection . getIntExtNamesP2Selection . hierDiffToGenesets . make.p2.app . minMaxScale . namedNames . p2.generate.dr.go . p2.generate.dr.go.web . p2.generate.go . p2.generate.go.web.fromGOEnv . p2.generate.go.web . p2.generate.human.go . p2.generate.human.go.web . p2.generate.mouse.go . p2.generate.mouse.go.web . p2.make.pagoda1.app . p2.metadata.from.factor . p2.toweb.hdea . p2ViewPagodaApp . pagoda.reduce.loading.redundancy . pagoda.reduce.redundancy . pagoda2WebApp . pagoda2WebApp_arrayToJSON . pagoda2WebApp_availableAspectsJSON . pagoda2WebApp_call . pagoda2WebApp_cellOrderJSON . pagoda2WebApp_cellmetadataJSON . pagoda2WebApp_geneInformationJSON . pagoda2WebApp_generateDendrogramOfGroups . pagoda2WebApp_generateEmbeddingStructure . pagoda2WebApp_generateGeneKnnJSON . pagoda2WebApp_getCompressedEmbedding . pagoda2WebApp_packCompressFloat64Array . pagoda2WebApp_packCompressInt32Array . pagoda2WebApp_readStaticFile . pagoda2WebApp_reducedDendrogramJSON . pagoda2WebApp_serializeToStaticFast . pagoda2WebApp_serverLog . pagoda2WebApp_sparseMatList . papply . pathway.pc.correlation.distance . plotMulticlassified . plotOneWithValues . plotSelectionOverlaps . projectKNNs . read.10x.matrices . read10xMatrix . readPagoda2SelectionAsFactor . readPagoda2SelectionFile . removeSelectionOverlaps . score.cells.nb0 . score.cells.nb1 . score.cells.puram . sgdBatches . show.app . sn . subsetSignatureToData . tp2c.view.pathways . validateSelectionsObject . view.aspects . webP2proc . winsorize.matrix . writeGenesAsPagoda2Selection . writePagoda2SelectionFile .
Some associated R codes: Pagoda2.R . RcppExports.R . cell.scoring.R . helpers.R . largeVis.R . p1_liftover.R . p1app4p2.R . pagoda2WebApp.R . pagodaWebHelpers.R . pagodaWebSelections.R . pipelineHelpers.R . Full pagoda2 package functions and examples
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