CRMetrics

07-05-2026

Cell Ranger output filtering and metrics visualisation

Introduction

This package was developed to visualize metrics from 10x Cell Ranger for single-cell (or single-nucleus) RNA-seq data. This has been expanded to include preprocessing of single-cell RNA-seq data, and include 10x Flex, multiome, and Parse technologies.

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:

• data.path: A path to a directory containing sample-wise directories with outputs from cellranger count. Can also be NULL. Can also be a vector of multiple paths.
• cms: A list with count matrices. Must be named with sample IDs. Can also be NULL
• metadata: Can either be 1) a data.frame, or 2) a path to a table file (separator should be set with the sep.meta argument), or 3) NULL. For 1) and 2) the object must contain named columns, and one column has to be named sample containing sample IDs. Sample IDs must match the directory names in data.path or names of cms unless both these are NULL. In case of 3), a minimal metadata object is created from names in data.path or names of cms.
• technology: Will default to 10x, but can also be 10xflex, 10xmultiome, parse

Vignette

For usage, please see the vignette

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. We also provide the option to output a Python script to be run in a separate environment, e.g. from terminal.

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]

It is also possible to use easyRef to create a citation for most common reference tools: easyRef::createRef("CRMetrics", filename = "CRMetrics.ris")