cellGeometry: ultra-fast single-cell deconvolution of bulk RNA-Seq using a geometric solution
Authors/Creators
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Lau, Rachel
(Contact person)1
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Çubuk, Cankut
(Contact person)1
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Spiliopoulou, Athina
(Annotator)2
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Martínez-Paz, Pedro
(Annotator)1
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Surace, Anna E. A.
(Annotator)1
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Fossati-Jimack, Liliane
(Annotator)1
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Raychaudhuri, Soumya
(Annotator)3
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Pitzalis, Costantino
(Annotator)1, 4
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Lewis, Myles J.
(Contact person)1, 5
- 1. Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Queen Mary University of London, and Barts NIHR Biomedical Research Centre & Barts Health NHS Trust, London, UK
- 2. Usher Institute, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, Scotland
- 3. Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- 4. IRCCS Istituto Clinico Humanitas, Via Manzoni 56, Rozzao, Milan, Italy
- 5. Digital Environment Research Institute, Queen Mary University of London, London, UK
Description
cellGeometry manuscript
This repository contains scripts for the cellGeometry manuscript
cellGeometry package is available on CRAN.
A vignette has been provided with instructions for installation of the package and necessary dependencies as well as basic analysis of the Cell Typist dataset via creation of a simulated pseudo-bulk dataset.
Another vignette also provides detailed instructions for merging simulated pseudo-bulk from 2 brain atlas snRNA-Seq data files and walks users through analysis of this dataset.
Data availability
Single-cell datasets for AMP phase 1 synovium are available from ImmPort accession code SDY998.
Single-cell datasets for Cell Typist are available from https://cellxgene.cziscience.com/collections/62ef75e4-cbea-454e-a0ce-998ec40223d3
Single-cell datasets for Tabula Sapiens are available from https://cellxgene.cziscience.com/collections/e5f58829-1a66-40b5-a624-9046778e74f5
Single-cell datasets for the Human Brain Cell Atlas is available from https://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443
The PEAC RA blood and synovium bulk RNA-Seq datasets, R4RA and STRAP bulk RA synovium RNA-Seq datasets are available from ArrayExpress under accession codes E-MTAB-6141, E-MTAB-11611 and E-MTAB-13733.
Files
EMR-bioinformatics/cellGeometry_manuscript-cellGeometry_manuscript.zip
Files
(16.2 MB)
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Additional details
Related works
- Is supplement to
- Software: https://github.com/EMR-bioinformatics/cellGeometry_manuscript/tree/cellGeometry_manuscript (URL)