Publications and citations

Citing STEGO.R

Science Advance (under consideration)

Print print bioRxiv

1. STEGO.R: an application to aid in scRNA-seq and scTCR-seq processing and analysis (V1)

2. T cell receptor-centric perspective to multimodal single-cell data analysis (V2)

Citing other related research

if you use the STEGO.R wrap around for the QC, we recommend also citing these other tools that made STEGO.R workflow possible.

1. Seurat Hao et al. (2023). Dictionary learning for integrative, multimodal, and scalable single-cell analysis. Nature Biotechnology, Seurat V5.

2. scGate Andreatta, M., Berenstein, A. J., & Carmona, S. J. (2022). “scGate: marker-based purification of cell types from heterogeneous single-cell RNA-seq datasets.” _Bioinformatics_, 38, 2642-2644. scGate.

3. clustcrdist Sebastiaan Valkiers (2024). clustcrdist tool. clustcrdist.

4. IMW-DETECT ImmuneWatch (IMW)-DETECT (Version 1.0) tool (2024; Available at: https://www.immunewatch.com/detect)

5. TCRex

   Gielis, S., Moris, P., Bittremieux, W., De Neuter, N., Ogunjimi, B., Laukens, K., & Meysman, P. (2019). Detection of Enriched T Cell Epitope Specificity in Full T Cell Receptor Sequence Repertoires. _Frontiers in Immunology_, 10, Article 2820. TCRex DOI.