getH5Paths

internal

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.

Rasmus Rydbirk

CRMetrics

Cell Ranger Output Filtering and Metrics Visualization

Fabienne Kick

Henrietta Holze

Xian Xin

getH5Paths function

<dl><dt>data.path</dt>
<dd>character Path for directory containing sample-wise directories with Cell Ranger count outputs</dd>
<dt>samples</dt>
<dd>character Sample names to include (default = NULL)</dd>
<dt>type</dt>
<dd>character Type of H5 files to get paths for, one of "raw", "filtered" (Cell Ranger count outputs), "cellbender" (raw CellBender outputs), "cellbender_filtered" (CellBender filtered outputs) (default = "type")</dd></dl>

Arguments

Get H5 file paths — getH5Paths

<dl>

<dt>data.path</dt>
<dd>character Path for directory containing sample-wise directories with Cell Ranger count outputs</dd>


<dt>samples</dt>
<dd>character Sample names to include (default = NULL)</dd>


<dt>type</dt>
<dd>character Type of H5 files to get paths for, one of "raw", "filtered" (Cell Ranger count outputs), "cellbender" (raw CellBender outputs), "cellbender_filtered" (CellBender filtered outputs) (default = "type")</dd>

</dl>

Get H5 file paths

getH5Paths: Get H5 file paths

Description

Usage

Arguments