This repo contains the code and associated files for "Multiomics Analysis of Metabolic Reprogramming by the Hypoxia Response Pathway", currently found on biorxiv.
The repo is organized into folders with self-descriptive names. For example, code contains the code used to process the data, perform analysis, and make figures. Likewise, data contains the data files used during the analysis. Note that some data files are missing because they are too large to place here and must be generated by running the code.
The code was run using R 4.1.3 and RStudio version 2022.02.01 Build 461. The code is compatible with R versions >4.0.0
Prior to running the code, download the following files and place them in the data folder.
ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_28/GRCh38.p12.genome.fa.gz ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_28/gencode.v28.annotation.gff3.gz
Each RMD file in the rmarkdown folder can be run independently. These files should be executed from their source folder - rmarkdown.
worm_TFB_comp.Rmd- Find HIF1 binding sites in CHIP peaks in worm.human_TFB_comp.Rmd- Analysis of human orthologs of worm HIF1 binding sites and analysis of HRE elements.overlap_with_modENCODE.Rmd- Analysis of overlap of other TF binding sites with HIF1 binding sites.chipseq_overlap.Rmd- A general purpose script to identify overlap between CHIP-seq peaks.deg_edgeR_analysis_luperchio.Rmd- Analysis of DEG from edgeR data (Leperchio 2021 method)