setup_progress_bar

Setup progress bar for batch processing

A normalization method for single-cell UMI count data using a
variance stabilizing transformation. The transformation is based on a
negative binomial regression model with regularized parameters. As part of the
same regression framework, this package also provides functions for
batch correction, and data correction. See Hafemeister and Satija (2019)
<doi:10.1186/s13059-019-1874-1>, and Choudhary and Satija (2022) <doi:10.1186/s13059-021-02584-9>
for more details.

Saket Choudhary

sctransform

Variance Stabilizing Transformations for Single Cell UMI Data

Christoph Hafemeister

Rahul Satija

setup_progress_bar function

<dl><dt>n_items</dt>
<dd>Total number of items to process</dd>
<dt>bin_size</dt>
<dd>Size of each batch/bin</dd>
<dt>verbosity</dt>
<dd>An integer specifying the verbosity level: 0 (silent), 1 (messages only), or 2 (messages and progress bars)</dd></dl>

Arguments

Setup progress bar for batch processing — setup_progress_bar

<dl>

<dt>n_items</dt>
<dd>Total number of items to process</dd>


<dt>bin_size</dt>
<dd>Size of each batch/bin</dd>


<dt>verbosity</dt>
<dd>An integer specifying the verbosity level: 0 (silent), 1 (messages only), or 2 (messages and progress bars)</dd>

</dl>

setup_progress_bar: Setup progress bar for batch processing

Description

Usage

Value

Arguments