CRMetrics

14/10/2022

Cell Ranger output filtering and metrics visualisation

Installation

To install the latest version, use

install.packages("devtools")
devtools::install_github("khodosevichlab/CRMetrics")

Initialization

A CRMetrics object can be initialized in different ways using CRMetrics$new(). 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
• 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.

Vignette

For usage, please see the vignette (code.

Python integrations

CRMetrics makes use of several Python packages, most of them through the reticulate package in R. For these to work, we included an example workflow in the vignette.

Cite

To cite this work, please run citation(CRMetrics).