Other packages > Find by keyword >

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 05 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
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

msm  
Multi-State Markov and Hidden Markov Models in Continuous Time
Functions for fitting continuous-time Markov and hidden Markov multi-state models to longitudinal d ...
Download / Learn more Package Citations See dependency  
envirem  
Generation of ENVIREM Variables
Generation of bioclimatic rasters that are complementary to the typical 19 bioclim variables. ...
Download / Learn more Package Citations See dependency  
quickcode  
Quick and Essential 'R' Tricks for Better Scripts
The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to im ...
Download / Learn more Package Citations See dependency  
crossurr  
Cross-Fitting for Doubly Robust Evaluation of High-Dimensional Surrogate Markers
Doubly robust methods for evaluating surrogate markers as outlined in: Agniel D, Hejblum BP, Thiebau ...
Download / Learn more Package Citations See dependency  
ibb  
R Wrapper for Istanbul Municipality Open Data Portal
Call wrappers for Istanbul Metropolitan Municipality's Open Data Portal (Turkish: Istanbul B ...
Download / Learn more Package Citations See dependency  

27,268

R Packages

233,548

Dependencies

72,590

Author Associations

27,205

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA