This the tutorial for running Cicero and TOBIAS packages on single cell ATAC data generated from cellranger.
The complete code has already been shared in the paper: scMultiomics_identifies_shared_and_distinct_pathways_in_Picks_and_Alzheimers_disease GitHub. Here is a more organized tutorial, and shortly we will provide a wrapper package to summarize the in-between steps for user eaiser to handle the data between all those tools .
To support the paper, we have built a database for checking the prediction of TF binding difference between two dementia and their age-matched control; and a package for easy running multiple code before/during TOBIAS and integrating co-accessibility results from Cicero.
Bentsen, M., Goymann, P., Schultheis, H. et al. ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation. Nat Commun 11, 4267 (2020). https://doi.org/10.1038/s41467-020-18035-1
Shi, Das & Morabito et al. Single-nucleus multi-omics identifies shared and distinct pathways in Pick’s and Alzheimer’s disease.
Zechuan Shi @rootze from Swarup lab at UCI
Samuel Morabito @smorabit from Swarup lab at UCI
Zechuan Shi @rootze created analysis documents that combine code
Programming software:
- R v4.1.1 and above
- Python v3.6 and above
Tools_Software:
- Signac (v1.9.0)
- ArchRtoSignac (v1.0.4)
- Seurat (v4.4.0)
- Cicero ()
- TOBIAS (v0.14.0)
In case of any issues/questions/comments, please check out the Issues. Otherwise, please write an issue for any questions here.