standard_fraction_design

<p>An example <code>fraction_design</code> table for a standard NR-seq experiment with
s^4U labeling. This table tells <code>EstimateFractions</code> that there are two
populations of reads, one with high T-to-C mutation content and one
with low T-to-C mutation content</p>

datasets

A complete rewrite and reimagining of 'bakR' (see 'Vock et al.' (2025) <doi:10.1371/journal.pcbi.1013179>).
Designed to support a wide array of analyses of nucleotide recoding RNA-seq (NR-seq) datasets of any
type, including TimeLapse-seq/SLAM-seq/TUC-seq, Start-TimeLapse-seq (STL-seq),
TT-TimeLapse-seq (TT-TL-seq), and subcellular NR-seq. 'EZbakR' extends
standard NR-seq standard NR-seq mutational modeling to support multi-label analyses
(e.g., 4sU and 6sG dual labeling), and implements an improved hierarchical model to better
account for transcript-to-transcript variance in metabolic label incorporation.
'EZbakR' also generalized dynamical systems modeling of NR-seq data to support analyses
of premature mRNA processing and flow between subcellular compartments. Finally,
'EZbakR' implements flexible and well-powered comparative analyses of all
estimated parameters via design matrix-specified generalized linear modeling.

Isaac Vock

EZbakR

Analyze and Integrate Any Type of Nucleotide Recoding RNA-Seq
Data

standard_fraction_design function


<div class="section" id="standard-fraction-design">
<h3><code>standard_fraction_design</code></h3><p></p><p>
</p><p>A tibble with 2 rows and 2 columns:</p><dl>
<dt>TC</dt>
<dd><p>Boolean denoting if population represented by that row has high T-to-C mutational content</p></dd><p></p><p><dt>present</dt>
<dd><p>Boolean denoting if population represented by that row is expected to be present in this dataset</p></dd></p><p>
</p></dl><p></p><p></p></div>


Format

Standard fraction_design table for EstimateFractions — standard_fraction_design


<div class='section' id='standard-fraction-design'>
<h3><code>standard_fraction_design</code></h3>


<p>A tibble with 2 rows and 2 columns:</p><dl>
<dt>TC</dt>
<dd><p>Boolean denoting if population represented by that row has high T-to-C mutational content</p></dd>

<dt>present</dt>
<dd><p>Boolean denoting if population represented by that row is expected to be present in this dataset</p></dd>


</dl>

</div>


standard_fraction_design: Standard `fraction_design` table for `EstimateFractions`

Description

Usage

Arguments

Format

`standard_fraction_design`