Dataset Information
GExcite - A start-to-end framework for single-cell gene expression, hashing, and antibody analysis.
Ontology highlight
ABSTRACT: Summary
Recently, CITE-seq emerged as a multimodal single-cell technology capturing gene expression and surface protein information from the same single-cells, which allows unprecedented insights into disease mechanisms and heterogeneity, as well as immune cell profiling. Multiple single-cell profiling methods exist, but they are typically focussed on either gene expression or antibody analysis, not their combination. Moreover, existing software suites are not easily scalable to a multitude of samples. To this end, we designed gExcite, a start-to-end workflow that provides both gene and antibody expression analysis, as well as hashing deconvolution. Embedded in the Snakemake workflow manager, gExcite facilitates reproducible and scalable analyses. We showcase the output of gExcite on a study of different dissociation protocols on PBMC samples.Availability
gExcite is open source available on github at https://github.com/ETH-NEXUS/gExcite_pipeline. The software is distributed under the GNU General Public License 3 (GPL3).Supplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Grob L
PROVIDER: S-EPMC10229235 | biostudies-literature | 2023 May
REPOSITORIES: biostudies-literature
Publications
gExcite: a start-to-end framework for single-cell gene expression, hashing, and antibody analysis.
Bioinformatics (Oxford, England) 20230501 5
<h4>Summary</h4>Recently, CITE-seq emerged as a multimodal single-cell technology capturing gene expression and surface protein information from the same single cells, which allows unprecedented insights into disease mechanisms and heterogeneity, as well as immune cell profiling. Multiple single-cell profiling methods exist, but they are typically focused on either gene expression or antibody analysis, not their combination. Moreover, existing software suites are not easily scalable to a multitu ...[more]