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# Protocols-4pub

## *Reusable code collection*

##### 26 April, 2021

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

---

*声明：该项目仅供学习用途，请共同遵守[开源协议](https://github.com/sajuukLyu/Protocols-4pub/blob/main/LICENSE)，禁止用于商业盈利。未经作者同意请勿转载至其它媒体。*

---

Integrated step-by-step vignettes present on the [wiki](https://github.com/sajuukLyu/Protocols-4pub/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 description

- Preprocess pipeline

| file name                                                    | description                                                  |
| ------------------------------------------------------------ | ------------------------------------------------------------ |
| [bulkATACpre.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/a_PreprocessPipeline/bulkATACpre.R) | Preprocess pipelines for bulk ATAC-seq [*(vignettes)*](https://sajuuklyu.github.io/Protocols-4pub/exampleData/ATAC/bulkATACpre.html) |
| [bulkRNApre.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/a_PreprocessPipeline/bulkRNApre.R) | Preprocess pipelines for bulk RNA-seq [*(vignettes)*](https://sajuuklyu.github.io/Protocols-4pub/exampleData/RNA/bulkRNApre.html) |
| [ChIPpre.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/a_PreprocessPipeline/ChIPpre.R) | Preprocess pipelines for ChIP-seq                            |
| [WGBSpre.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/a_PreprocessPipeline/WGBSpre.R) | Preprocess pipelines for Whole Genome Bisulfite Sequencing   |

- Downstream analysis script

| file name                                                    | omics | description                                           |
| ------------------------------------------------------------ | ----- | ----------------------------------------------------- |
| [downloadData.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/b_DownstreamAnalysisScript/downloadData.R) | any   | Download data from public databases                   |
| [bulkRNAana_1_loadCount.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/b_DownstreamAnalysisScript/bulkRNAana_1_loadCount.R) | RNA   | Load multiple results and convert to count matrix     |
| [bulkRNAana_2a_DESeq.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/b_DownstreamAnalysisScript/bulkRNAana_2a_DESeq.R) | RNA   | Perform DESeq analysis (for sample without replicate) |
| [bulkRNAana_2b_DESeq2.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/b_DownstreamAnalysisScript/bulkRNAana_2b_DEseq2.R) | RNA   | Perform DESeq2 analysis (for sample with replicates)  |
| [bulkRNAana_3_GO.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/b_DownstreamAnalysisScript/bulkRNAana_3_GO.R) | RNA   | Perform GO analysis                                   |
| [bulkATACana_1_QC.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/b_DownstreamAnalysisScript/bulkATACana_1_QC.R) | ATAC  | Quality control                                       |
| [bulkATACana_2_loadCount.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/b_DownstreamAnalysisScript/bulkATACana_2_loadCount.R) | ATAC  | Load data and convert to peak matrix                  |
| [bulkATACana_3_annotatePeak.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/b_DownstreamAnalysisScript/bulkATACana_3_annotatePeak.R) | ATAC  | Annotate peaks to nearest genes                       |
| [bulkATACana_4_GO.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/b_DownstreamAnalysisScript/bulkATACana_4_GO.R) | ATAC  | Perform GO analysis                                   |
| [bulkATACana_5_peakTF.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/b_DownstreamAnalysisScript/bulkATACana_5_peakTF.R) | ATAC  | Perform gene regulate network analysis                |

- Visualization script

| file name                                                    | omics | description                                    |
| ------------------------------------------------------------ | ----- | ---------------------------------------------- |
| [Visulz_bulkRNA_PCA.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkRNA_PCA.R) | RNA   | PCA plot for samples                           |
| [Visulz_bulkRNA_MAplot.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkRNA_MAplot.R) | RNA   | MA plot for DEGs between group of samples      |
| [Visulz_bulkRNA_volcano.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkRNA_volcano.R) | RNA   | Volcano plot for DEGs between group of samples |
| [Visulz_bulkRNA_heatmap.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkRNA_heatmap.R) | RNA   | Heatmap of given genes for samples             |
| [Visulz_bulkRNA_GO.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkRNA_GO.R) | RNA   | GO plot for DEGs                               |
| [Visulz_bulkATAC_trackPlot.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkATAC_trackPlot.R) | ATAC  | Track plot for samples                         |
| [Visulz_bulkATAC_PCA.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkATAC_PCA.R) | ATAC  | PCA plot for samples                           |
| [Visulz_bulkATAC_heatmapPeak.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkATAC_heatmapPeak.R) | ATAC  | Heatmap of given peaks for samples             |
| [Visulz_bulkATAC_heatmapTrack.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkATAC_heatmapTrack.R) | ATAC  | Heatmap of given peak tracks for samples       |
| [Visulz_bulkATAC_peakAnnoDisp.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkATAC_peakAnnoDisp.R) | ATAC  | Histogram for peak annotation distribution     |
| [Visulz_bulkATAC_motifEnrich.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkATAC_motifEnrich.R) | ATAC  | Scatter plot for enriched TFs for peak sets    |
| [Visulz_bulkATAC_network.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkATAC_network.R) | ATAC  | Network plot for peak sets                     |





















	a/README.md		b/README.md
1	# Protocols-4pub	1	# Protocols-4pub
2		2
3	## Reusable code collection	3	## Reusable code collection
4		4
5	##### 26 April, 2021	5	##### 26 April, 2021
6		6
7	Multi-omics analysis protocols concluded by SajuukLyu <lvyulin@pku.edu.cn>.	7	Multi-omics analysis protocols concluded by SajuukLyu <lvyulin@pku.edu.cn>.
8		8
9	---	9	---
10		10
11	声明：该项目仅供学习用途，请共同遵守[开源协议](https://github.com/sajuukLyu/Protocols-4pub/blob/main/LICENSE)，禁止用于商业盈利。未经作者同意请勿转载至其它媒体。	11	声明：该项目仅供学习用途，请共同遵守[开源协议](https://github.com/sajuukLyu/Protocols-4pub/blob/main/LICENSE)，禁止用于商业盈利。未经作者同意请勿转载至其它媒体。
12		12
13	---	13	---
14		14
15	Integrated step-by-step vignettes present on the [wiki](https://github.com/sajuukLyu/Protocols-4pub/wiki).	15	Integrated step-by-step vignettes present on the [wiki](https://github.com/sajuukLyu/Protocols-4pub/wiki).
16		16
17	These files including three main parts:	17	These files including three main parts:
18		18
19	- Preprocess pipeline (etc. bulkRNA, bulkATAC, ChIP, WGBS ...)	19	- Preprocess pipeline (etc. bulkRNA, bulkATAC, ChIP, WGBS ...)
20		20
21	These R scripts are designed to generate a directory tree containing ordered directories for intermediate data and Linux bash scripts for each step.	21	These R scripts are designed to generate a directory tree containing ordered directories for intermediate data and Linux bash scripts for each step.
22	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.	22	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.
23		23
24	- Downstream analysis script (etc. DEG, GO, GSEA ...)	24	- Downstream analysis script (etc. DEG, GO, GSEA ...)
25		25
26	These scripts are the framework of different analyses designed to cope with the most simple scene of biology analysis.	26	These scripts are the framework of different analyses designed to cope with the most simple scene of biology analysis.
27		27
28	- Visualization script (etc. heatmap, PCA plot, Venn plot, track plot ...)	28	- Visualization script (etc. heatmap, PCA plot, Venn plot, track plot ...)
29		29
30	These scripts can generate some plots suitable for articles with very few post processing.	30	These scripts can generate some plots suitable for articles with very few post processing.
31		31
32	### File description	32	### File description
33		33
34	- Preprocess pipeline	34	- Preprocess pipeline
35		35
36	\| file name \| description \|	36	\| file name \| description \|
37	\| ------------------------------------------------------------ \| ------------------------------------------------------------ \|	37	\| ------------------------------------------------------------ \| ------------------------------------------------------------ \|
38	\| [bulkATACpre.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/a_PreprocessPipeline/bulkATACpre.R) \| Preprocess pipelines for bulk ATAC-seq [(vignettes)](https://sajuuklyu.github.io/Protocols-4pub/exampleData/ATAC/bulkATACpre.html) \|	38	\| [bulkATACpre.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/a_PreprocessPipeline/bulkATACpre.R) \| Preprocess pipelines for bulk ATAC-seq [(vignettes)](https://sajuuklyu.github.io/Protocols-4pub/exampleData/ATAC/bulkATACpre.html) \|
39	\| [bulkRNApre.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/a_PreprocessPipeline/bulkRNApre.R) \| Preprocess pipelines for bulk RNA-seq [(vignettes)](https://sajuuklyu.github.io/Protocols-4pub/exampleData/RNA/bulkRNApre.html) \|	39	\| [bulkRNApre.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/a_PreprocessPipeline/bulkRNApre.R) \| Preprocess pipelines for bulk RNA-seq [(vignettes)](https://sajuuklyu.github.io/Protocols-4pub/exampleData/RNA/bulkRNApre.html) \|
40	\| [ChIPpre.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/a_PreprocessPipeline/ChIPpre.R) \| Preprocess pipelines for ChIP-seq \|	40	\| [ChIPpre.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/a_PreprocessPipeline/ChIPpre.R) \| Preprocess pipelines for ChIP-seq \|
41	\| [WGBSpre.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/a_PreprocessPipeline/WGBSpre.R) \| Preprocess pipelines for Whole Genome Bisulfite Sequencing \|	41	\| [WGBSpre.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/a_PreprocessPipeline/WGBSpre.R) \| Preprocess pipelines for Whole Genome Bisulfite Sequencing \|
42		42
43	- Downstream analysis script	43	- Downstream analysis script
44		44
45	\| file name \| omics \| description \|	45	\| file name \| omics \| description \|
46	\| ------------------------------------------------------------ \| ----- \| ----------------------------------------------------- \|	46	\| ------------------------------------------------------------ \| ----- \| ----------------------------------------------------- \|
47	\| [downloadData.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/b_DownstreamAnalysisScript/downloadData.R) \| any \| Download data from public databases \|	47	\| [downloadData.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/b_DownstreamAnalysisScript/downloadData.R) \| any \| Download data from public databases \|
48	\| [bulkRNAana_1_loadCount.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/b_DownstreamAnalysisScript/bulkRNAana_1_loadCount.R) \| RNA \| Load multiple results and convert to count matrix \|	48	\| [bulkRNAana_1_loadCount.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/b_DownstreamAnalysisScript/bulkRNAana_1_loadCount.R) \| RNA \| Load multiple results and convert to count matrix \|
49	\| [bulkRNAana_2a_DESeq.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/b_DownstreamAnalysisScript/bulkRNAana_2a_DESeq.R) \| RNA \| Perform DESeq analysis (for sample without replicate) \|	49	\| [bulkRNAana_2a_DESeq.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/b_DownstreamAnalysisScript/bulkRNAana_2a_DESeq.R) \| RNA \| Perform DESeq analysis (for sample without replicate) \|
50	\| [bulkRNAana_2b_DESeq2.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/b_DownstreamAnalysisScript/bulkRNAana_2b_DEseq2.R) \| RNA \| Perform DESeq2 analysis (for sample with replicates) \|	50	\| [bulkRNAana_2b_DESeq2.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/b_DownstreamAnalysisScript/bulkRNAana_2b_DEseq2.R) \| RNA \| Perform DESeq2 analysis (for sample with replicates) \|
51	\| [bulkRNAana_3_GO.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/b_DownstreamAnalysisScript/bulkRNAana_3_GO.R) \| RNA \| Perform GO analysis \|	51	\| [bulkRNAana_3_GO.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/b_DownstreamAnalysisScript/bulkRNAana_3_GO.R) \| RNA \| Perform GO analysis \|
52	\| [bulkATACana_1_QC.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/b_DownstreamAnalysisScript/bulkATACana_1_QC.R) \| ATAC \| Quality control \|	52	\| [bulkATACana_1_QC.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/b_DownstreamAnalysisScript/bulkATACana_1_QC.R) \| ATAC \| Quality control \|
53	\| [bulkATACana_2_loadCount.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/b_DownstreamAnalysisScript/bulkATACana_2_loadCount.R) \| ATAC \| Load data and convert to peak matrix \|	53	\| [bulkATACana_2_loadCount.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/b_DownstreamAnalysisScript/bulkATACana_2_loadCount.R) \| ATAC \| Load data and convert to peak matrix \|
54	\| [bulkATACana_3_annotatePeak.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/b_DownstreamAnalysisScript/bulkATACana_3_annotatePeak.R) \| ATAC \| Annotate peaks to nearest genes \|	54	\| [bulkATACana_3_annotatePeak.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/b_DownstreamAnalysisScript/bulkATACana_3_annotatePeak.R) \| ATAC \| Annotate peaks to nearest genes \|
55	\| [bulkATACana_4_GO.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/b_DownstreamAnalysisScript/bulkATACana_4_GO.R) \| ATAC \| Perform GO analysis \|	55	\| [bulkATACana_4_GO.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/b_DownstreamAnalysisScript/bulkATACana_4_GO.R) \| ATAC \| Perform GO analysis \|
56	\| [bulkATACana_5_peakTF.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/b_DownstreamAnalysisScript/bulkATACana_5_peakTF.R) \| ATAC \| Perform gene regulate network analysis \|	56	\| [bulkATACana_5_peakTF.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/b_DownstreamAnalysisScript/bulkATACana_5_peakTF.R) \| ATAC \| Perform gene regulate network analysis \|
57		57
58	- Visualization script	58	- Visualization script
59		59
60	\| file name \| omics \| description \|	60	\| file name \| omics \| description \|
61	\| ------------------------------------------------------------ \| ----- \| ---------------------------------------------- \|	61	\| ------------------------------------------------------------ \| ----- \| ---------------------------------------------- \|
62	\| [Visulz_bulkRNA_PCA.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkRNA_PCA.R) \| RNA \| PCA plot for samples \|	62	\| [Visulz_bulkRNA_PCA.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkRNA_PCA.R) \| RNA \| PCA plot for samples \|
63	\| [Visulz_bulkRNA_MAplot.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkRNA_MAplot.R) \| RNA \| MA plot for DEGs between group of samples \|	63	\| [Visulz_bulkRNA_MAplot.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkRNA_MAplot.R) \| RNA \| MA plot for DEGs between group of samples \|
64	\| [Visulz_bulkRNA_volcano.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkRNA_volcano.R) \| RNA \| Volcano plot for DEGs between group of samples \|	64	\| [Visulz_bulkRNA_volcano.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkRNA_volcano.R) \| RNA \| Volcano plot for DEGs between group of samples \|
65	\| [Visulz_bulkRNA_heatmap.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkRNA_heatmap.R) \| RNA \| Heatmap of given genes for samples \|	65	\| [Visulz_bulkRNA_heatmap.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkRNA_heatmap.R) \| RNA \| Heatmap of given genes for samples \|
66	\| [Visulz_bulkRNA_GO.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkRNA_GO.R) \| RNA \| GO plot for DEGs \|	66	\| [Visulz_bulkRNA_GO.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkRNA_GO.R) \| RNA \| GO plot for DEGs \|
67	\| [Visulz_bulkATAC_trackPlot.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkATAC_trackPlot.R) \| ATAC \| Track plot for samples \|	67	\| [Visulz_bulkATAC_trackPlot.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkATAC_trackPlot.R) \| ATAC \| Track plot for samples \|
68	\| [Visulz_bulkATAC_PCA.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkATAC_PCA.R) \| ATAC \| PCA plot for samples \|	68	\| [Visulz_bulkATAC_PCA.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkATAC_PCA.R) \| ATAC \| PCA plot for samples \|
69	\| [Visulz_bulkATAC_heatmapPeak.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkATAC_heatmapPeak.R) \| ATAC \| Heatmap of given peaks for samples \|	69	\| [Visulz_bulkATAC_heatmapPeak.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkATAC_heatmapPeak.R) \| ATAC \| Heatmap of given peaks for samples \|
70	\| [Visulz_bulkATAC_heatmapTrack.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkATAC_heatmapTrack.R) \| ATAC \| Heatmap of given peak tracks for samples \|	70	\| [Visulz_bulkATAC_heatmapTrack.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkATAC_heatmapTrack.R) \| ATAC \| Heatmap of given peak tracks for samples \|
71	\| [Visulz_bulkATAC_peakAnnoDisp.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkATAC_peakAnnoDisp.R) \| ATAC \| Histogram for peak annotation distribution \|	71	\| [Visulz_bulkATAC_peakAnnoDisp.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkATAC_peakAnnoDisp.R) \| ATAC \| Histogram for peak annotation distribution \|
72	\| [Visulz_bulkATAC_motifEnrich.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkATAC_motifEnrich.R) \| ATAC \| Scatter plot for enriched TFs for peak sets \|	72	\| [Visulz_bulkATAC_motifEnrich.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkATAC_motifEnrich.R) \| ATAC \| Scatter plot for enriched TFs for peak sets \|
73	\| [Visulz_bulkATAC_network.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkATAC_network.R) \| ATAC \| Network plot for peak sets \|	73	\| [Visulz_bulkATAC_network.R](https://github.com/sajuukLyu/Protocols-4pub/blob/main/c_VisualizationScript/Visulz_bulkATAC_network.R) \| ATAC \| Network plot for peak sets \|
74		74
75	### Pipeline
76
77	- bulk RNA-seq
78
79	<img src="mermaidPlot\bulkRNApre.svg" align=center>
80
81	- bulk ATAC-seq
82
83	<img src="mermaidPlot\bulkATACpre.svg" align=center>
84
85	- ChIP-seq
86
87	<img src="mermaidPlot\ChIPpre.svg" align=center>
88
89	- WGBS
90
91	<img src="mermaidPlot\WGBSpre.svg" align=center>
92
93