CRMetrics
Cell Ranger Output Filtering and Metrics Visualization
Rasmus Rydbirk, Fabienne Kick, Henrietta Holze
Last update: 1 September 2023
Copyright license: GNU General Public License, version 3.0
Software version identifier: 0.2.3, 0.2.2, 0.3.0
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.
- Massively parallel digital transcriptional profiling of single cells
- SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data
- Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender
- Integrated analysis of multimodal single-cell data
- Joint analysis of heterogeneous single-cell RNA-seq dataset collections
- Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data
- JonathanShor/DoubletDetection: doubletdetection v4.2
