README (original) (raw)

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 usingCRMetrics$new(). Either data.path orcms 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 beNULL. 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 thesep.meta argument), or 3) NULL. For 1) and 2) the object must contain named columns, and one column has to be namedsample containing sample IDs. Sample IDs must match the directory names in data.path or names of cmsunless 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, 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\]