# nf-core/scdownstream: Citations

## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)

> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.

## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)

> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.

## Base pipelines

- [panpipes](https://doi.org/10.1101/2023.03.11.532085)

  > Curion F, Rich-Griffin C, Agarwal D, et al. Panpipes: a pipeline for multiomic single-cell and spatial transcriptomic data analysis. Published online December 18, 2023:2023.03.11.532085. doi:10.1101/2023.03.11.532085

- [scFlow](https://doi.org/10.1101/2021.08.16.456499)

  > Khozoie C, Fancy N, Marjaneh MM, Murphy AE, Matthews PM, Skene N. scFlow: A Scalable and Reproducible Analysis Pipeline for Single-Cell RNA Sequencing Data. Published online August 19, 2021:2021.08.16.456499. doi:10.1101/2021.08.16.456499

- [SIMBA](https://github.com/Mye-InfoBank/SIMBA)

  > Trummer, N. et al. 2024. SIMBA (Single-cell Integration Methods pipeline for Big Atlases)

- [YASCP](https://github.com/wtsi-hgi/yascp)
  > Ozols, M. et al. 2023. YASCP (Yet Another Single Cell Pipeline)

## Pipeline tools

- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)

  > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

- [singleR](https://pubmed.ncbi.nlm.nih.gov/30643263/)

  > Aran D, Looney AP, Liu L, Wu E, Fong V, Hsu A, et al. Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage. Nat Immunol. 2019;20(2):163-172. doi: 10.1038/s41590-018-0276-y. Epub 2018 Dec 17. PubMed PMID: 30531964; PubMed Central PMCID: PMC6350770.

- [CyteType](https://github.com/NygenAnalytics/cytetype)

  > Ahuja G et al. CyteType: multi-agent LLM-driven cell type annotation for single-cell RNA-seq. bioRxiv 2025. doi:10.1101/2025.11.06.686964.

- [Seurat](https://pubmed.ncbi.nlm.nih.gov/29608179/)

  > Butler A, Hoffman P, Smibert P, Papalexi E, Satija R. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol. 2018 Apr;36(5):411-420. doi: 10.1038/nbt.4096. Epub 2018 Mar 12. PubMed PMID: 29608179; PubMed Central PMCID: PMC5965097.

- [celldex](https://pubmed.ncbi.nlm.nih.gov/30643263/)

  > Aran D, Looney AP, Liu L, Wu E, Fong V, Hsu A, Chak S, Naikawadi RP, Wolters PJ, Abate AR, Butte AJ, Bhattacharya M (2019). “Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage.” Nat. Immunol., 20, 163-172. doi:10.1038/s41590-018-0276-y.

- [anndataR](https://anndatar.data-intuitive.com/)

  > Cannoodt R, Zappia L, Morgan M, Deconinck L (2025). anndataR: AnnData interoperability in R. R package version 0.99.0

- [scanpy](https://pubmed.ncbi.nlm.nih.gov/29409532/)

  > Wolf, F. A., Angerer, P., & Theis, F. J. (2018). SCANPY: large-scale single-cell gene expression data analysis. Genome biology, 19(1), 15. https://doi.org/10.1186/s13059-017-1382-0

- [LIANA+](https://doi.org/10.1038/s41556-024-01469-w)

  > Dimitrov D, Schäfer PSL, Farr E, et al. LIANA+ provides an all-in-one framework for cell–cell communication inference. Nat Cell Biol. 2024;26:1613–1622. doi:10.1038/s41556-024-01469-w

- [Tensor-cell2cell](https://doi.org/10.1038/s41467-022-31369-2)

  > Armingol E, Baghdassarian HM, Martino C, et al. Context-aware deconvolution of cell–cell communication with Tensor-cell2cell. Nat Commun. 2022;13:3665. doi:10.1038/s41467-022-31369-2

- [scarches](https://pypi.org/project/scArches/)

  > Lotfollahi, M., Naghipourfar, M., Luecken, M.D. et al. Mapping single-cell data to reference atlases by transfer learning. Nat Biotechnol 40, 121–130 (2022). https://doi.org/10.1038/s41587-021-01001-7

- [scDblFinder](https://pubmed.ncbi.nlm.nih.gov/35118618/)

  > Germain P, Lun A, Garcia Meixide C, Macnair W, Robinson M. Doublet identification in single-cell sequencing data using scDblFinder. F1000Res. 2022;11:979. doi: 10.12688/f1000research.73600.2.

## Software packaging/containerisation tools

- [Anaconda](https://anaconda.com)

  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.

- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)

  > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.

- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)

  > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)

  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.

- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)

  > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.
