destiny: diffusion maps for large-scale single-cell data in R
- PMID: 26668002
- DOI: 10.1093/bioinformatics/btv715
destiny: diffusion maps for large-scale single-cell data in R
Abstract
: Diffusion maps are a spectral method for non-linear dimension reduction and have recently been adapted for the visualization of single-cell expression data. Here we present destiny, an efficient R implementation of the diffusion map algorithm. Our package includes a single-cell specific noise model allowing for missing and censored values. In contrast to previous implementations, we further present an efficient nearest-neighbour approximation that allows for the processing of hundreds of thousands of cells and a functionality for projecting new data on existing diffusion maps. We exemplarily apply destiny to a recent time-resolved mass cytometry dataset of cellular reprogramming.
Availability and implementation: destiny is an open-source R/Bioconductor package "bioconductor.org/packages/destiny" also available at www.helmholtz-muenchen.de/icb/destiny A detailed vignette describing functions and workflows is provided with the package.
Contact: carsten.marr@helmholtz-muenchen.de or f.buettner@helmholtz-muenchen.de
Supplementary information: Supplementary data are available at Bioinformatics online.
© The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
Similar articles
-
Diffusion maps for high-dimensional single-cell analysis of differentiation data.Bioinformatics. 2015 Sep 15;31(18):2989-98. doi: 10.1093/bioinformatics/btv325. Epub 2015 May 21. Bioinformatics. 2015. PMID: 26002886
-
Sincell: an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq.Bioinformatics. 2015 Oct 15;31(20):3380-2. doi: 10.1093/bioinformatics/btv368. Epub 2015 Jun 22. Bioinformatics. 2015. PMID: 26099264 Free PMC article.
-
clustComp, a bioconductor package for the comparison of clustering results.Bioinformatics. 2017 Dec 15;33(24):4001-4003. doi: 10.1093/bioinformatics/btx532. Bioinformatics. 2017. PMID: 28961761 Free PMC article.
-
An end-to-end workflow for multiplexed image processing and analysis.Nat Protoc. 2023 Nov;18(11):3565-3613. doi: 10.1038/s41596-023-00881-0. Epub 2023 Oct 10. Nat Protoc. 2023. PMID: 37816904 Review.
-
Orchestrating single-cell analysis with Bioconductor.Nat Methods. 2020 Feb;17(2):137-145. doi: 10.1038/s41592-019-0654-x. Epub 2019 Dec 2. Nat Methods. 2020. PMID: 31792435 Free PMC article. Review.
Cited by
-
Bone morphogenic protein-4 availability in the cardiac microenvironment controls inflammation and fibrosis in autoimmune myocarditis.Nat Cardiovasc Res. 2024 Mar;3(3):301-316. doi: 10.1038/s44161-024-00432-0. Epub 2024 Feb 19. Nat Cardiovasc Res. 2024. PMID: 39196111
-
Compound-SNE: Comparative alignment of t-SNEs for multiple single-cell omics data visualisation.Bioinformatics. 2024 Jul 25;40(7):btae471. doi: 10.1093/bioinformatics/btae471. Online ahead of print. Bioinformatics. 2024. PMID: 39052868 Free PMC article.
-
Single-cell atlas of the human brain vasculature across development, adulthood and disease.Nature. 2024 Aug;632(8025):603-613. doi: 10.1038/s41586-024-07493-y. Epub 2024 Jul 10. Nature. 2024. PMID: 38987604 Free PMC article.
-
Tumour vasculature at single-cell resolution.Nature. 2024 Aug;632(8024):429-436. doi: 10.1038/s41586-024-07698-1. Epub 2024 Jul 10. Nature. 2024. PMID: 38987599
-
Primary nasal influenza infection rewires tissue-scale memory response dynamics.Immunity. 2024 Aug 13;57(8):1955-1974.e8. doi: 10.1016/j.immuni.2024.06.005. Epub 2024 Jul 3. Immunity. 2024. PMID: 38964332
MeSH terms
Grants and funding
LinkOut - more resources
Full Text Sources
Other Literature Sources