The latest breakthrough in single-cell omics is on multi-modal profiling of different biomolecule species in individual cells. Among the fast evolving biotechnologies developed for multi-modal profiling, cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) is attracting attention, especially in the field of immunology, given its ability to simultaneously quantify global gene expression and cellular proteins using RNA-sequencing and antibody-derived tags (ADTs) on single cells. While the additional protein marker information brought about by ADTs is extremely valuable, new biological insights can only be gained by developing analytic methods that fully take advantage of the complementarity between mRNA and ADT expression measured in CITE-seq.
To address this, we developed a streamlined pipeline–CiteFuse–that consists of a suite of tools for the integration and the downstream analysis of CITE-seq data. In this workshop, we will provide a hands-on experience to the CiteFuse package and cover all the steps including doublet detection, modality integration, cell type clustering, differential RNA and ADT expression analysis, ADT evaluation, and ligand–receptor interaction analysis on a publicly available CITE-seq dataset. We also demonstrate the applicability of CiteFuse package on other multi-modal data types by applying our pipeline on the recently developed ASAP-seq data.
This vignette provides a more complete description of the various tools in CiteFuse and will serve as the basis of our workshop.
An example for a 55-minute workshop:
|Data processing and integration||15m|
|Application of CiteFuse on ASAP-seq||5m|
|Wrap-up and Conclusions||5m|