Analysis of single cell datasets using dreamlet software

Here we present analysis code, data and results from 4 public datasets.

Novel Alzheimer's snRNA-seq data

• Generated as part of this work, and currently public
• PsychAD project and data
• Analysis code: PsychAD_r0_analysis.Rmd
  • Results: PsychAD_r0_analysis.html
  • Figures: 5, 6, S6-S8
• Analysis code to compare methods: PsychAD_r0_compare_methods.Rmd
  • Results: PsychAD_r0_compare_methods.html
  • Figures: S11-S18

Reanalysis of external Alzheimer's snRNA-seq data

• Mathys, et al. Cell (2023)
• Data: MIT / ROSMAP study
• Analysis code: Mathys_2023_Major_Cell_Type.Rmd
  • Results: Mathys_2023_Major_Cell_Type.html
• Analysis code: PsychAD_Mathys.Rmd
  • Results: PsychAD_Mathys.html
  • Figures: S9,S10

Bone metastases from prostate cancer

• Kfoury, et al. Cancer Cell (2021)
• Download and format data: Kfoury_CancerCell_2021_get_data.Rmd
• Public data in H5AD format Kfoury_CancerCell_2021.h5ad
• Analysis code: Kfoury_CancerCell_2021.Rmd
  • Results: Kfoury_CancerCell_2021.html
  • Figures: 4, S5

Response to COVID-19 severity

• COMBAT Consortium. Cell (2023)
• Data: Zenodo
• Analysis code: COVID_combat_minor.Rmd
  • Results: COVID_combat_minor.html
  • Figures: 3, S4