Single cell lineage reconstruction using distance-based algorithms and the R package, DCLEAR.
BMC Bioinformatics
; 23(1): 103, 2022 Mar 24.
Article
in En
| MEDLINE
| ID: mdl-35331133
ABSTRACT
BACKGROUND:
DCLEAR is an R package used for single cell lineage reconstruction. The advances of CRISPR-based gene editing technologies have enabled the prediction of cell lineage trees based on observed edited barcodes from each cell. However, the performance of existing reconstruction methods of cell lineage trees was not accessed until recently. In response to this problem, the Allen Institute hosted the Cell Lineage Reconstruction Dream Challenge in 2020 to crowdsource relevant knowledge from across the world. Our team won sub-challenges 2 and 3 in the challenge competition.RESULTS:
The DCLEAR package contained the R codes, which was submitted in response to sub-challenges 2 and 3. Our method consists of twosteps:
(1) distance matrix estimation and (2) the tree reconstruction from the distance matrix. We proposed two novel methods for distance matrix estimation as outlined in the DCLEAR package. Using our method, we find that two of the more sophisticated distance methods display a substantially improved level of performance compared to the traditional Hamming distance method. DCLEAR is open source and freely available from R CRAN and from under the GNU General Public License, version 3.CONCLUSIONS:
DCLEAR is a powerful resource for single cell lineage reconstruction.Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Algorithms
/
Software
Language:
En
Journal:
BMC Bioinformatics
Journal subject:
INFORMATICA MEDICA
Year:
2022
Document type:
Article
Affiliation country: