Protocols-4pub

Reusable code collection

Multi-omics analysis protocols concluded by SajuukLyu lvyulin@pku.edu.cn.

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Integrated step-by-step vignettes present on the wiki.

These files including three main parts:

Preprocess pipeline (etc. bulkRNA, bulkATAC, ChIP, WGBS ...)

These R scripts are designed to generate a directory tree containing ordered directories for intermediate data and Linux bash scripts for each step.
In convenient to submit jobs to different nodes of a computer cluster at same time, commands for multiple samples can be divided to several batches and than submit together.
Downstream analysis script (etc. DEG, GO, GSEA ...)

These scripts are the framework of different analyses designed to cope with the most simple scene of biology analysis.
Visualization script (etc. heatmap, PCA plot, Venn plot, track plot ...)

These scripts can generate some plots suitable for articles with very few post processing.

file name	description
bulkATACpre.R	Preprocess pipelines for bulk ATAC-seq (vignettes)
bulkRNApre.R	Preprocess pipelines for bulk RNA-seq (vignettes)
ChIPpre.R	Preprocess pipelines for ChIP-seq
WGBSpre.R	Preprocess pipelines for Whole Genome Bisulfite Sequencing

file name	omics	description
downloadData.R	any	Download data from public databases
bulkRNAana_1_loadCount.R	RNA	Load multiple results and convert to count matrix
bulkRNAana_2a_DESeq.R	RNA	Perform DESeq analysis (for sample without replicate)
bulkRNAana_2b_DESeq2.R	RNA	Perform DESeq2 analysis (for sample with replicates)
bulkRNAana_3_GO.R	RNA	Perform GO analysis
bulkATACana_1_QC.R	ATAC	Quality control
bulkATACana_2_loadCount.R	ATAC	Load data and convert to peak matrix
bulkATACana_3_annotatePeak.R	ATAC	Annotate peaks to nearest genes
bulkATACana_4_GO.R	ATAC	Perform GO analysis
bulkATACana_5_peakTF.R	ATAC	Perform gene regulate network analysis

file name	omics	description
Visulz_bulkRNA_PCA.R	RNA	PCA plot for samples
Visulz_bulkRNA_MAplot.R	RNA	MA plot for DEGs between group of samples
Visulz_bulkRNA_volcano.R	RNA	Volcano plot for DEGs between group of samples
Visulz_bulkRNA_heatmap.R	RNA	Heatmap of given genes for samples
Visulz_bulkRNA_GO.R	RNA	GO plot for DEGs
Visulz_bulkATAC_trackPlot.R	ATAC	Track plot for samples
Visulz_bulkATAC_PCA.R	ATAC	PCA plot for samples
Visulz_bulkATAC_heatmapPeak.R	ATAC	Heatmap of given peaks for samples
Visulz_bulkATAC_heatmapTrack.R	ATAC	Heatmap of given peak tracks for samples
Visulz_bulkATAC_peakAnnoDisp.R	ATAC	Histogram for peak annotation distribution
Visulz_bulkATAC_motifEnrich.R	ATAC	Scatter plot for enriched TFs for peak sets
Visulz_bulkATAC_network.R	ATAC	Network plot for peak sets