Read10X_Image

A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.

Paul Hoffman

Seurat

Tools for Single Cell Genomics

Andrew Butler

Saket Choudhary

Charlotte Darby

Jeff Farrell

Christoph Hafemeister

Yuhan Hao

Austin Hartman

Jaison Jain

Madeline Kowalski

Efthymia Papalexi

Patrick Roelli

Rahul Satija

Karthik Shekhar

Avi Srivastava

Tim Stuart

Kristof Torkenczy

Shiwei Zheng

Satija Lab and Collaborators 

Read10X_Image function

<dl><dt>image.dir</dt>
<dd>Path to directory with 10X Genomics visium image data;
should include files <code>tissue_lowres_image.png</code>,</dd>
<dt>image.name</dt>
<dd>The file name of the image. Defaults to tissue_lowres_image.png.
<code>scalefactors_json.json</code> and <code>tissue_positions_list.csv</code></dd>
<dt>filter.matrix</dt>
<dd>Filter spot/feature matrix to only include spots that
have been determined to be over tissue.</dd>
<dt>...</dt>
<dd>Ignored for now</dd></dl>

Arguments

Load a 10X Genomics Visium Image — Read10X_Image

<dl>

<dt>image.dir</dt>
<dd>Path to directory with 10X Genomics visium image data;
should include files <code>tissue_lowres_image.png</code>,</dd>


<dt>image.name</dt>
<dd>The file name of the image. Defaults to tissue_lowres_image.png.
<code>scalefactors_json.json</code> and <code>tissue_positions_list.csv</code></dd>


<dt>filter.matrix</dt>
<dd>Filter spot/feature matrix to only include spots that
have been determined to be over tissue.</dd>


<dt>...</dt>
<dd>Ignored for now</dd>

</dl>

Load a 10X Genomics Visium Image

Read10X_Image: Load a 10X Genomics Visium Image

Description

Usage

Value

Arguments

See Also