Repo for Manuscript:
Bustoros, M., Anand, S., et al. "Genetic subtypes of smoldering multiple myeloma are associated with distinct pathogenic phenotypes and clinical outcomes." Nature communications 13.1 (2022): 1-10.
Link to pre-print.
Link to Nature Communications publication.
Contact: Shankara Anand - sanand@broadinstitute.org
Table of DNA-based SMM subtypes
Note: we included in this table the names used in previous iterations and seen in the code base.
Repo Structure:
data - see ./data/README.md
funcs - folder with python/R helper functions or scripts written
Fig1
1_clustering.ipynb: notebook with clustering, QC, fisher exact tests for DNA features2_misc.ipynb: misc cohort plots3*_mutational_signatures.ipynb: mutational signature analysis with subtypes
Fig2
1_process_rna.ipynb: python notebook describing RNA processing & QC2_diffexp_pathways_rna.ipynb: R notebook with differential expression, fGSEA, & other plots for Fig2 & related supplements
Fig3
1_clinical_classifier.ipynb: subtype classifier for clinical outcomes- Run
00-fig-km.R,01-fig-traj.R, then02-fig-pairs.R