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Description

Cell Ranger Output Filtering and Metrics Visualization.

Sample and cell filtering as well as visualisation of output metrics from 'Cell Ranger' by Grace X.Y. Zheng et al. (2017) <doi:10.1038/ncomms14049>. '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) <doi:10.1093/gigascience/giaa151> or 'CellBender' by Stephen J Fleming et al. (2022) <doi:10.1101/791699>. Furthermore, it is possible to preprocess data using 'Pagoda2' by Nikolas Barkas et al. (2021) <https://github.com/kharchenkolab/pagoda2> or 'Seurat' by Yuhan Hao et al. (2021) <doi:10.1016/j.cell.2021.04.048> followed by embedding of cells using 'Conos' by Nikolas Barkas et al. (2019) <doi:10.1038/s41592-019-0466-z>. Finally, doublets can be detected using 'scrublet' by Samuel L. Wolock et al. (2019) <doi:10.1016/j.cels.2018.11.005> or 'DoubletDetection' by Gayoso et al. (2020) <doi:10.5281/zenodo.2678041>. In the end, cells are filtered based on user input for use in downstream applications.

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:

  • 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.

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]

Metadata

Version

0.3.0

License

Unknown

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