This repo contains all code needed to generate figures and supplementary figures from Subramaniam et al., 2019. It is orgaanized by figure number from the paper. They are organized as follows:
Figure 1: Cell type proportion differences
Figure 2: Variance partitioning
Figuer 3: Myeloid effects in SLE
Figure 4: Lymphoid effects in SLE
Figure 5: Genetics of SLE
Figure 6: SLE Flares
Once you've cloned the repo, make sure you create a h5ad directory and download the h5ad files from the following: https://ucsf.box.com/s/tds2gotok3lyeanlrt13prj40am5w720.
Raw sequencing (.fastq) and alignment (.bam) files can be found here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE137029.