All data analyzes have been performed with R version 4.4.0 and tested also on 4.0.5.
As for libraries version with R 4.4.0 :
- crayon : 1.5.2
- GenomicRanges : 1.56.0
- dplyr : 1.1.4
- ggplot2 : 3.5.1
- data.table : 1.15.4
- ggpubr : 0.6.0
- karyoploteR : 1.30.0
- rtracklayer : 1.64.0
- corrr : 0.4.4
- GGally : 2.2.1
- ComplexHeatmap : 2.20.0
- plyr : 1.8.9
- CAinterprTools : 1.1.0
- RColorBrewer : 1.1.3
- ggVennDiagram : 1.5.2
- ggdendro: 0.2.0
and for R 4.0.5 :
- crayon : 1.5.2
- GenomicRanges : 1.42.0
- dplyr : 1.1.4
- ggplot2 : 3.4.2
- data.table : 1.15.2
- ggpubr : 0.6.0
- karyoploteR : 1.16.0
- rtracklayer : 1.50.0
- corrr : 0.4.4
- GGally : 2.2.1
- ComplexHeatmap : 2.20.0
- plyr : 1.8.9
- CAinterprTools : 1.1.0
- RColorBrewer : 1.1.3
- ggVennDiagram : 1.2.2
- ggdendro: 0.2.0
Download required files with src/00_init_project.sh Then use related .sh script to align raw data for each sequencing type
In order to generate chromsome arms bed positions use lift_over_chr_arms.R script.
Those data can be obtained through tiled_genome_bed.R script
Union and intersection of peaksets can be retrieved using bedtools.sh script.
To transform .bm tad separation score files to bigwig please use bm2bw.R.
Use g2ih5_To_cm_rds.R to turn g2i.h5 matrices into .rds R format
After performing union & intersection of peakset, use computeMatrixProfile.sh script to compute ChIP-seq bigwig signal profile around peaks of interest.
This repo stores bioinformatic R scripts used to generate manuscript figures. All scripts start with this line that has to be modified accordingly to the path used to clone this repo :
setwd(dir = "config/src/R/github/")
Data must be stored in /data folder along with the scripts . It must contain the following folders :
- data/ChIPseq : Contains bed, bigwig and ${ip}_${condition}_newzs_prof.txt profile files.
- data/RNAseq : Contains deseq2_counts_all_conditions.txt and matrecap_genes_ce11.gtf files
- data/HiC : Contains all contact matrices (norm.KR.g2i.h5, obs_exp.g2i.h5, norm.KR.cm.rds, obs_exp.cm.rds), all bigwig for Eigen vectors (pca1.bw), bigwig for TAD separation scores tad_score.bw and TAD in bed format
The following additional files must be stored in ChIPseq folder :
- ce11_noMT.bed
- ce11_tiled_10kb.bed
- ce11_tiled_1kb.bed
- ce11_tiled_25kb.bed
- ce11_tiled_5kb.bed
- chr_arms_ce11.bed
- genes_ce11.bed
If you prefer storing them elsewhere, you will need to adapt scripts for manuscript figures accordingly.