Repo for imputing sex, cell line, and other metadata labels from refine-bio data and examining the results for the paper Large-scale Labeling and Assessment of Sex Bias in Publicly Available Expression data by Flynn, Chang, and Altman.

Data files are not included for space limits, but final inferred labels are located here and will be available in refine.bio. This analysis focuses on human and mouse data; in principle it should be applicable to other organisms previously but this has yet to be examined.

The code/ directory is setup as follows:

• 01_metadata/ - code for extracting metadata labels from refine-bio, cleaning, and mapping
• 02_expression/ - code for extracting microarray and RNA-seq data from compendia
• 03_models/ - code for building models
• 04_apply_models/ - code for applying models
• 05_analysis/ - preliminary analyses

Within directory, scripts are numbered according to order to run. Most scripts are setup as:
Rscript <script_name> <organism>

Many also take as a final argument an idx for chunking/array scripts.

R package dependencies: tidyverse, data.table, glmnet.
For microarray extraction, data is converted to gctx format using the cmappy Python package.

Please contact erflynn -AT- stanford -DOT- edu with questions.