f.nonconst

The standard mass action kinetics model of gene expression arises from the differential equation
\(df/dt = s(t) - d(t) f(t)\), with s(t) being the synthesis rate at time t, d(t) the degradation rate at time t and \(f0=f(0)\) (the abundance at time 0).
Here, both s and d have the following form \(s(t)=so+sf \cdot t^{se}\).

Nucleotide conversion sequencing experiments have been
developed to add a temporal dimension to RNA-seq and single-cell RNA-seq. Such
experiments require specialized tools for primary processing such as GRAND-SLAM,
(see 'Jürges et al' <doi:10.1093/bioinformatics/bty256>) and specialized tools for
downstream analyses. 'grandR' provides a comprehensive toolbox for quality control,
kinetic modeling, differential gene expression analysis and visualization of such data.

Florian Erhard

grandR

Comprehensive Analysis of Nucleotide Conversion Sequencing Data

Teresa Rummel

Lygeri Sakellaridi

Kevin Berg

f.nonconst function

<dl><dt>t</dt>
<dd>time in h (can be a vector)</dd>
<dt>f0</dt>
<dd>the abundance at time t=0</dd>
<dt>s</dt>
<dd>the synthesis rate (see details)</dd>
<dt>d</dt>
<dd>the degradation rate (see details)</dd></dl>

Arguments

Function to compute the abundance of new or old RNA at time t for non-constant rates. — f.nonconst

<dl>

<dt>t</dt>
<dd>time in h (can be a vector)</dd>


<dt>f0</dt>
<dd>the abundance at time t=0</dd>


<dt>s</dt>
<dd>the synthesis rate (see details)</dd>


<dt>d</dt>
<dd>the degradation rate (see details)</dd>

</dl>

f.nonconst: Function to compute the abundance of new or old RNA at time t for non-constant rates.

Description

Usage

Value

Arguments

Details

See Also