D1 and D2 nuclear and whole cell RNAseq analyses

• 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