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CRMetrics  

Cell Ranger Output Filtering and Metrics Visualization
View on CRAN: Click here


Download and install CRMetrics package within the R console
Install from CRAN:
install.packages("CRMetrics")

Install from Github:
library("remotes")
install_github("cran/CRMetrics")

Install by package version:
library("remotes")
install_version("CRMetrics", "0.3.2")



Attach the package and use:
library("CRMetrics")
Maintained by
Rasmus Rydbirk
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2022-11-30
Latest Update: 2024-11-08
Description:
Sample and cell filtering as well as visualisation of output metrics from 'Cell Ranger' by Grace X.Y. Zheng et al. (2017) . 'CRMetrics' allows for easy plotting of output metrics across multiple samples as well as comparative plots including statistical assessments of these. 'CRMetrics' allows for easy removal of ambient RNA using 'SoupX' by Matthew D Young and Sam Behjati (2020) or 'CellBender' by Stephen J Fleming et al. (2022) . Furthermore, it is possible to preprocess data using 'Pagoda2' by Nikolas Barkas et al. (2021) or 'Seurat' by Yuhan Hao et al. (2021) followed by embedding of cells using 'Conos' by Nikolas Barkas et al. (2019) . Finally, doublets can be detected using 'scrublet' by Samuel L. Wolock et al. (2019) or 'DoubletDetection' by Gayoso et al. (2020) . In the end, cells are filtered based on user input for use in downstream applications.
How to cite:
Rasmus Rydbirk (2022). CRMetrics: Cell Ranger Output Filtering and Metrics Visualization. R package version 0.3.2, https://cran.r-project.org/web/packages/CRMetrics. Accessed 04 Jun. 2026.
Previous versions and publish date:
0.2.2 (2022-11-30 12:40), 0.2.3 (2022-12-14 12:30), 0.3.0 (2023-09-01 11:00), 0.3.2 (2024-11-08 01:20)
Other packages that cited CRMetrics R package
View CRMetrics citation profile
Other R packages that CRMetrics depends, imports, suggests or enhances
Complete documentation for CRMetrics
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