This repo contains reports and scripts to perform exploratory data analysis of RNA-seq, ChIP-seq, and Cut&Run data on Ikzf1/3 KO samples in mouse NK cells. Some of the results included in these reports have been published in Nature Immunology.

Under the report/ folder, there are three Rmd files, containing the main analysis reports:

• report/Ikzf1_multi_omics.Rmd: this is the main script that reads in the results of several in-house RNA-seq, ChIP-seq (Ikzf3) and Cut&Run (Ikzf1) data, as well as several publicly available transcriptomics and epigenomics data sets, and attempts to explore the data using different visualisations and ana analysis aproches.
• report/Ikzf3_CnR_MACS2.Rmd: We ran MACS2 peak calling on the Cut&Run data, and have analysed it using nextflow, manual shell scripting as well as through the Galaxy. Here, I read in the results of my manual narrow peak calling, perform DB analysis using featureCount and edgeR, and additionally, I perform a quick comparison between the results obtained from nextflow and Galaxy.
• report/Ikzf3_CnR_csaw.Rmd: This report uses bam files and perform a window-based analysis through the csaw, rtracklayer, and edgeR packages.

Under the script/ folder, there are three scripts for QC and data visualisations:

• script/plotHeatmapExpr.R: a ComplexHeatmap-based custom function to generates heatmaps of gene expression and takes on row and column annotation
• script/PCA_plot.R: custom function to generate PCA plots using three PCs and annotates the percent variation explained by each PC on the plots.
• script/RLE_ggplot.R: a ggplot-based custom function to calculate and plot relative log expression in the transcriptomics data to examine unwanted variation.