References
Software and Tools
Cell Ranger
10x Genomics. (2024). Cell Ranger Software Suite.
Cell Ranger ATAC
10x Genomics. (2024). Cell Ranger ATAC Software Suite.
FastQC
Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data.
https://github.com/s-andrews/FastQC
MultiQC
Ewels, Philip, et al. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics, 32(19), 3047-3048.
https://github.com/MultiQC/MultiQC
CellBender
Fleming, Stephen J., et al. (2023). Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender. Nature Methods, 20(9), 1323-1335.
https://github.com/broadinstitute/CellBender
cellsnp-lite
Huang, Xianjie, and Yuanhua Huang. (2021). Cellsnp-lite: an efficient tool for genotyping single cells. Bioinformatics, 37(23), 4569-4571.
https://github.com/single-cell-genetics/cellsnp-lite
Vireo
Sinha, R., et al. (2020). Vireo: a scalable approach to analyze single-cell RNA-seq data. Bioinformatics, 36(14), 4247-4249.
https://github.com/single-cell-genetics/vireo
AMULET
Thibodeau, Asa, et al. (2021). AMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data. Genome Biology, 22(1), 1-19.
https://github.com/UcarLab/AMULET
mgatk
Lareau, Caleb A., et al. (2021). Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling. Nature Biotechnology, 39(4), 451-461.
https://github.com/caleblareau/mgatk
KITE
Gehring, Jase, et al. (2020). Highly multiplexed single-cell RNA-seq by DNA oligonucleotide tagging of cellular proteins. Nature Biotechnology, 38(1), 35-38.
https://github.com/pachterlab/kite
Additional Resources
Group Information
Learning Resources
- Single-cell Assay Library Structures - Comprehensive resource on library structures
- NBISweden scRNA-seq Workshop - Tutorial on scRNA-seq analysis
- Dendrou Lab scRNA-seq Pipeline - Oxford lab's processing pipeline
- nf-core scRNA-seq Pipeline - Nextflow community pipeline
Citation
If you use OSCAR in your research, please cite:
Knight, O. (2025). OSCAR: Ollie's Single Cell Analysis for the Romagnani lab.
GitHub repository: https://github.com/ollieeknight/OSCAR
Contact
For questions or support:
- Email: oliver.knight@charite.de
- GitHub: https://github.com/ollieeknight/OSCAR