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.