R-CMD-check CRAN version CRAN downloads License: GPL-3

CRMetrics

05-07-2023

Cell Ranger output filtering and metrics visualisation

Installation

install.packages("remotes")
remotes::install_github("khodosevichlab/CRMetrics") # CRAN version
remotes::install_github("khodosevichlab/CRMetrics", ref = "dev") # developer version

Initialization

A CRMetrics object can be initialized in different ways using CRMetrics$new(). Either data.path or cms must be provided. The most important arguments are:

Vignette

For usage, please see the vignette / code.

Python integrations

CRMetrics makes use of several Python packages, some of them through the reticulate package in R, please see the included example workflow in the vignette.

Cite

To cite this work, please run citation("CRMetrics") or cite our preprint:

Fabienne Lorena Kick, Henrietta Holze, Rasmus Rydbirk, Konstantin Khodosevich: CRMetrics - an R package for Cell Ranger Filtering and Metrics Visualisation, 06 July 2023, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-2853524/v1]