Analysis scripts used in the analysis of Seq-Well and CyTOF datasets of Ebola virus infected PBMCs for the manuscript Single-cell profiling of Ebola virus infection in vivo reveals viral and host transcriptional dynamics. See https://github.com/dylkot/dropSeqPipe-dak for the pipeline used to map the single-cell RNA-Seq reads and to generate the expression count matrices. Image above is the graphical abstract from the manuscript.
- setup.sh - commands to create the conda environment used for all of the analysis
- Code - libraries used throughout the analysis
- Analysis - Jupyter notebooks for running the pipelines and generating the figures in the manuscript
- InVivo - Analysis of Seq-Well and CyTOF data from Ebola infected rhesus macaques
- ExVivo - Analysis of Seq-Well data from PBMCs extracted from rhesus macaques and infected ex vivo
- HCA_BoneMarrow - Comparison of EVD data with healthy human bone marrow and PBMCs
- Human_EVD_CyTOF - Re-analysis of published CyTOF data of human EVD cases (McElroy et al., 2020)