capture.image.10x

This function takes 10X image data files and converts them to proper file format for iCellR.

A toolkit that allows scientists to work with data from single cell sequencing technologies such as scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptomics (ST). Single (i) Cell R package ('iCellR') provides unprecedented flexibility at every step of the analysis pipeline, including normalization, clustering, dimensionality reduction, imputation, visualization, and so on. Users can design both unsupervised and supervised models to best suit their research. In addition, the toolkit provides 2D and 3D interactive visualizations, differential expression analysis, filters based on cells, genes and clusters, data merging, normalizing for dropouts, data imputation methods, correcting for batch differences, pathway analysis, tools to find marker genes for clusters and conditions, predict cell types and pseudotime analysis. See Khodadadi-Jamayran, et al (2020) <doi:10.1101/2020.05.05.078550> and Khodadadi-Jamayran, et al (2020) <doi:10.1101/2020.03.31.019109> for more details.

Alireza Khodadadi-Jamayran

iCellR

Analyzing High-Throughput Single Cell Sequencing Data

Joseph Pucella

Hua Zhou

Nicole Doudican

John Carucci

Adriana Heguy

Boris Reizis

Aristotelis Tsirigos

capture.image.10x function

<dl><dt>dir.10x</dt>
<dd>A directory that includes the 10X image files (scalefactors_json.json, tissue_lowres_image.png and tissue_positions_list.csv).</dd></dl>

Arguments

Read 10X image data — capture.image.10x

<dl>

<dt>dir.10x</dt>
<dd>A directory that includes the 10X image files (scalefactors_json.json, tissue_lowres_image.png and tissue_positions_list.csv).</dd>

</dl>

capture.image.10x: Read 10X image data

Description

Usage

Value

Arguments