CRAN/E | CRMetrics

CRMetrics

Cell Ranger Output Filtering and Metrics Visualization

Installation

About

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) 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.

github.com/khodosevichlab/CRMetrics
Bug report File report

Key Metrics

Version 0.3.0
R ≥ 4.0.0
Published 2023-09-01 227 days ago
Needs compilation? no
License GPL-3
CRAN checks CRMetrics results

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Maintainer

Maintainer

Rasmus Rydbirk

rrydbirk@bmb.sdu.dk

Authors

Rasmus Rydbirk

aut / cre

Fabienne Kick

aut

Henrietta Holze

aut

Xian Xin

ctb

Material

README
NEWS
Reference manual
Package source

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

CRMetrics archive

Depends

R ≥ 4.0.0

Imports

cowplot
dplyr
ggbeeswarm
ggplot2
ggpmisc
ggpubr
ggrepel
magrittr
Matrix
methods
R6
scales
sccore
sparseMatrixStats
stats
tibble
tidyr
utils

Suggests

conos
data.table
markdown
pagoda2
reticulate
rhdf5
Seurat
SoupX
testthat ≥ 3.0.0