process_sequence,phyDat-method

R codes for distance based cell lineage reconstruction. Our methods won both sub-challenges 2 and 3 of the Allen Institute Cell Lineage Reconstruction DREAM Challenge in 2020.
References: Gong et al. (2021) <doi:10.1016/j.cels.2021.05.008>, Gong et al. (2022) <doi:10.1186/s12859-022-04633-x>.

Il-Youp Kwak

DCLEAR

Distance Based Cell Lineage Reconstruction

Wuming Gong

process_sequence,phyDat-method function

<dl><dt>x</dt>
<dd>input data in phyDat format</dd>
<dt>division</dt>
<dd>cell division</dd>
<dt>dropout_character</dt>
<dd>Dropout character (default: '*')</dd>
<dt>default_character</dt>
<dd>Default character (default: '0')</dd>
<dt>deletion_character</dt>
<dd>Deletion character (default: '-')</dd></dl>

Arguments

Author

Process sequences — process_sequence,phyDat-method

<dl>

<dt>x</dt>
<dd>input data in phyDat format</dd>


<dt>division</dt>
<dd>cell division</dd>


<dt>dropout_character</dt>
<dd>Dropout character (default: '*')</dd>


<dt>default_character</dt>
<dd>Default character (default: '0')</dd>


<dt>deletion_character</dt>
<dd>Deletion character (default: '-')</dd>

</dl>

process_sequence,phyDat-method: Process sequences

Description

Usage

Value

Arguments

Author