This repository contains the code associated with the case studies from our paper "Differential detection workflows for multi-sample single-cell RNA-seq data" (TODO: add link).
The COVID dataset from Stephenson et al. (2021) can be downloaded programatically by running the first script of the Covid case study, 1_CovidCase_getdata.Rmd.
Alternatively, if you would like to avoid downloading these data, you can download intermediate data objects from Zenodo (TODO: add link) and place these in the Covid/objects/ directory. The file sce_Covid_Bcells.rds allows you to start the analysis from script 2_CovidCase_DGE.Rmd. Downloading the four other files from Zenodo and placing these in the objects directory allows you to start the analysis from scrip 4_CovidCase_downstream.Rmd.
The Lupus data from Perez et al. (2021) can be
downloaded from GEO using accession number
GSE174188. To run the case study code from start to end, download the GSE174188_CLUES1_adjusted.h5ad.gz file and place it in the Lupus/data-raw/ directory. Next, run the scripts 00-anndata-to-SCE.R, 01_lupus_prepare.Rmd and 02_lupus_case.Rmd in order.
Alternatively, if you would like to avoid downloading GSE174188_CLUES1_adjusted.h5ad.gz (11.7Gb), you can download intermediate data objects from Zenodo (TODO: add link) and place these in the Lupus/objects/ directory. The file lupus-SCE-cleaned.rds allows you to start the analysis from script 01_lupus_prepare.Rmd, the file sce_sep_filt.rds allows you to start the analysis from script 02_lupus_case.Rmd.