phyloFrame

Workflow for ancestry unbaised genetic signatures

Version

1.0

Leslie A Smith, James A Cahill, Kiley Graim

-- GnomAD VCF parsing done in leslie-smith1112/gnomad_vcf_parsing. Kept as seperate directory for now for simplicity in dependencies.

-- Files for pipeline: GnomAD file: https: https://gnomad.broadinstitute.org/downloads (gnomAD V2.1.1) HumanBase networks: https://hb.flatironinstitute.org/download (full networks; mammary epithelium, uterine endometrium, thyroid gland) Disease expression matrices and clinical info (cBioportal): https://www.cbioportal.org/datasets (brca_tcga_pan_can_atlas_2018.tar.gz, ucec_tcga_pan_can_atlas_2018.tar.gz, thca_tcga_pan_can_atlas_2018.tar.gz)

-- Scripts for figures used in the paper are in the ./figure_scripts directory.

Name		Name	Last commit message	Last commit date
Latest commit History 44 Commits
analysis		analysis
diseases		diseases
figure_scripts		figure_scripts
old_scripts		old_scripts
slurm_scripts		slurm_scripts
LICENSE		LICENSE
README.md		README.md
annotate_network.R		annotate_network.R
enhancedAF_calculations.R		enhancedAF_calculations.R
expression_elasticnet.R		expression_elasticnet.R
new_exomeAF_nosex_ordering.R		new_exomeAF_nosex_ordering.R
phyloFrame_main.R		phyloFrame_main.R
phyloFrame_run.R		phyloFrame_run.R
sample_selection.R		sample_selection.R