How to cite scprocess¶
If you use scprocess in your research, please cite our preprint.
scprocess relies on various open-source tools. Please consider citing the specific methods used in your analysis:
| Tool name | Citation |
|---|---|
| CellBender | Stephen J Fleming, Mark D Chaffin, Alessandro Arduini, Amer-Denis Akkad, Eric Banks, John C Marioni, Anthony A Philippakis, Patrick T Ellinor, and Mehrtash Babadi. Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender. Nat. Methods, 20(9):1323–1335, September 2023. |
| CellTypist | Chuan Xu, Martin Prete, Simone Webb, Laura Jardine, Benjamin J Stewart, Regina Hoo, Peng He, Kerstin B Meyer, and Sarah A Teichmann. Automatic cell-type harmonization and integration across human cell atlas datasets. Cell, 186(26):5876–5891.e20, December 2023. C Domínguez Conde, C Xu, L B Jarvis, D B Rainbow, S B Wells, T Gomes, S K Howlett, O Suchanek, K Polanski, H W King, L Mamanova, N Huang, P A Szabo, L Richardson, L Bolt, E S Fasouli, K T Mahbubani, M Prete, L Tuck, N Richoz, Z K Tuong, L Campos, H S Mousa, E J Needham, S Pritchard, T Li, R Elmentaite, J Park, E Rahmani, D Chen, D K Menon, O A Bayraktar, L K James, K B Meyer, N Yosef, M R Clatworthy, P A Sims, D L Farber, K Saeb-Parsy, J L Jones, and S A Teichmann. Cross-tissue immune cell analysis reveals tissue-specific features in humans. Science, 376(6594):eabl5197, May 2022. |
| DecontX | Shiyi Yang, Sean E Corbett, Yusuke Koga, Zhe Wang, W Evan Johnson, Masanao Yajima, and Joshua D Campbell. Decontamination of ambient RNA in single-cell RNA-seq with DecontX. Genome Biol., 21(1):57, March 2020. |
| DropletUtils | Aaron T L Lun, Samantha Riesenfeld, Tallulah Andrews, The Phuong Dao, Tomas Gomes, participants in the 1st Human Cell Atlas Jamboree, and John C Marioni. EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data. Genome Biol., 20(1):63, March 2019. Jonathan A Griffiths, Arianne C Richard, Karsten Bach, Aaron T L Lun, and John C Marioni. Detection and removal of barcode swapping in single-cell RNA-seq data. Nat. Commun., 9(1):2667, July 2018. |
| edgeR | Mark D Robinson, Davis J McCarthy, and Gordon K Smyth. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26(1):139–140, January 2010. Yunshun Chen, Lizhong Chen, Aaron T L Lun, Pedro L Baldoni, and Gordon K Smyth. edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets. Nucleic Acids Res., January 2025. |
| fgsea | Gennady Korotkevich, Vladimir Sukhov, Nikolay Budin, Boris Shpak, Maxim N Artyomov, and Alexey Sergushichev. Fast gene set enrichment analysis. bioRxiv, June 2016. |
| Harmony | Ilya Korsunsky, Nghia Millard, Jean Fan, Kamil Slowikowski, Fan Zhang, Kevin Wei, Yuriy Baglaenko, Michael Brenner, Po-Ru Loh, and Soumya Raychaudhuri. Fast, sensitive and accurate integration of single-cell data with harmony. Nat. Methods, 16(12):1289–1296, December 2019. |
| PAGA | F Alexander Wolf, Fiona K Hamey, Mireya Plass, Jordi Solana, Joakim S Dahlin, Berthold Göttgens, Nikolaus Rajewsky, Lukas Simon, and Fabian J Theis. PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells. Genome Biol., 20(1):59, March 2019. |
| RAPIDS-singlecell | Corey Nolet, Avantika Lal, Rajesh Ilango, Taurean Dyer, Rajiv Movva, John Zedlewski, and Johnny Israeli. Accelerating single-cell genomic analysis with GPUs. bioRxiv, May 2022. |
| SampleQC | Will Macnair and Mark Robinson. SampleQC: robust multivariate, multi-cell type, multi-sample quality control for single-cell data. Genome Biol., 24(1):23, February 2023. |
| Scanpy | F Alexander Wolf, Philipp Angerer, and Fabian J Theis. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol., December 2018. |
| scDblFinder | Pierre-Luc Germain, Aaron Lun, Will Macnair, and Mark D Robinson. Doublet identification in single-cell sequencing data using scDblFinder. F1000Res., 10:979, September 2021. |
| Seurat | Yuhan Hao, Tim Stuart, Madeline H Kowalski, Saket Choudhary, Paul Hoffman, Austin Hartman, Avi Srivastava, Gesmira Molla, Shaista Madad, Carlos Fernandez-Granda, and Rahul Satija. Dictionary learning for integrative, multimodal and scalable single-cell analysis. Nat. Biotechnol., 42(2):293–304, February 2024. Yuhan Hao, Stephanie Hao, Erica Andersen-Nissen, William M Mauck, 3rd, Shiwei Zheng, Andrew Butler, Maddie J Lee, Aaron J Wilk, Charlotte Darby, Michael Zager, Paul Hoffman, Marlon Stoeckius, Efthymia Papalexi, Eleni P Mimitou, Jaison Jain, Avi Srivastava, Tim Stuart, Lamar M Fleming, Bertrand Yeung, Angela J Rogers, Juliana M McElrath, Catherine A Blish, Raphael Gottardo, Peter Smibert, and Rahul Satija. Integrated analysis of multimodal single-cell data. Cell, 184(13):3573–3587.e29, June 2021. Tim Stuart, Andrew Butler, Paul Hoffman, Christoph Hafemeister, Efthymia Papalexi, William M Mauck, 3rd, Yuhan Hao, Marlon Stoeckius, Peter Smibert, and Rahul Satija. Comprehensive integration of single-cell data. Cell, 177(7):1888–1902.e21, June 2019. Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, and Rahul Satija. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat. Biotechnol., 36(5):411–420, May 2018. Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, and Aviv Regev. Spatial reconstruction of single-cell gene expression data. Nat. Biotechnol., 33(5):495–502, May 2015. |
| simpleaf | Dongze He and Rob Patro. Simpleaf: a simple, flexible, and scalable framework for single-cell data processing using alevin-fry. Bioinformatics, October 2023. |