- code_pipeline
- aracne.R: script for ARACNE co-expression calculations and hub network filtering
- count_to_norm_fc.R and count_to_norm_functions.R: load counts data and process with TMM/voom/limma pipeline
- de_gene_fc.R: limma DE scripts
- deseq2_from_fc_2018_04_23.R: DESeq2 code and PCA plots
- fastq_qc_align.py: python wrapper around alignment commands (and possibly also featurecounts if this needs heavy automating)
- featurecounts.R: load SAM information into a counts matrix using a reference GTF or one derived from the data
- gene_set_enrichment_gwas.R: GWAS filtering and gene set enrichment scripts
- intron_pct_calc.R: calculate percent intron per gene
- module_posthoc_analyses.R: plot gene kME and trait correlations
- pca_cluster_stats.R: calculate Euclidean distance to assess relative tightness on PCA
- variance_partition.R: calculate variance partition
- varpart_pretty_plots.R: various custom plotting attempts for variance_partition.R output
- wgcna.R: run WGCNA and plot results
- wgcna_plotting_functions.R: functions for plotting WGCNA results
- gene_sets
- human_to_mouse_orthologues.txt: ENSEMBL - gene ID maps for human and mouse genes along with confidence
- gwas_catalog: intermediate and final files for selecting GWAS genes for enrichment tests
- README.md
- This file