pagoda2
Single Cell Analysis and Differential Expression
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.
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CRAN Check Status
Show all 13 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check History
OK 12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 25, 2026
NOTE 12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 22, 2026
package dependencies
Packages suggested but not available for checking: 'GO.db', 'org.Dr.eg.db', 'org.Mm.eg.db', 'scde'
installed package size
installed size is 6.9Mb
sub-directories of 1Mb or more:
libs 5.1Mb
ERROR 11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 18, 2026
whether package can be installed
Installation failed. See 'd:/Rcompile/CRANpkg/local/4.6/pagoda2.Rcheck/00install.out' for details.
package dependencies
Packages suggested but not available for checking: 'GO.db', 'org.Dr.eg.db', 'org.Mm.eg.db', 'scde'
installed package size
installed size is 6.9Mb
sub-directories of 1Mb or more:
libs 5.1Mb
NOTE 10 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 10, 2026
package dependencies
Packages suggested but not available for checking: 'GO.db', 'org.Dr.eg.db', 'org.Mm.eg.db', 'scde'
installed package size
installed size is 6.9Mb
sub-directories of 1Mb or more:
libs 5.1Mb
ERROR 9 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 9, 2026
package dependencies
Package required but not available: ‘sccore’ Package suggested but not available for checking: ‘uwot’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Packages suggested but not available for checking: 'GO.db', 'org.Dr.eg.db', 'org.Mm.eg.db', 'scde'
installed package size
installed size is 6.9Mb
sub-directories of 1Mb or more:
libs 5.1Mb
NOTE 12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
package dependencies
Packages suggested but not available for checking: 'GO.db', 'org.Dr.eg.db', 'org.Mm.eg.db', 'scde'
installed package size
installed size is 6.9Mb
sub-directories of 1Mb or more:
libs 5.1Mb