| ---
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| license: cc-by-nc-nd-4.0
|
| ---
|
|
|
| # Directory Structure
|
|
|
| ```
|
| .
|
| ├── README.md
|
| ├── dpacman
|
| │ ├── data
|
| │ │ ├── README.md
|
| │ │ ├── chip_atlas
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| │ │ │ ├── full_data_loading.py
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| │ │ │ └── smaller_data_loading.py
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| │ │ ├── remap
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| │ │ │ ├── analyze.py
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| │ │ └── tfclust
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| │ │ ├── analyze.py
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| │ │ ├── api_download.py
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| │ │ ├── combine.py
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| │ │ ├── download.py
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| │ │ ├── figures
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| │ │ │ ├── seq_lengths_box.png
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| │ │ │ ├── seq_lengths_flanked_box.png
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| │ │ │ ├── seq_lengths_flanked_hist.png
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| │ │ │ ├── seq_lengths_flanked_xlog_box.png
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| │ │ │ ├── seq_lengths_flanked_xlog_hist.png
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| │ │ │ ├── seq_lengths_hist.png
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| │ │ │ ├── seq_lengths_xlog_box.png
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| │ │ │ └── seq_lengths_xlog_hist.png
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| │ │ ├── hg38_success_download.log
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| │ └── data_files
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| │ ├── processed
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| │ │ └── tfclust
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| │ │ ├── hg19
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| │ │ │ ├── encRegTfbsClustered_hg19_chr1.csv
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| │ │ │ └── logs
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| │ │ │ ├── completed.txt
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| │ │ │ ├── completed_worker_0.txt
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| │ │ │ ├── worker_0.log
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| │ │ └── hg38
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| │ │ ├── encRegTfbsClustered_hg38_chr1.csv
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| │ │ └── logs
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| │ │ ├── completed.txt
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| │ │ ├── completed_worker_0.txt
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| │ │ ├── worker_0.log
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| │ └── raw
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| │ ├── chip_atlas
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| │ │ └── experimentList.tab
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| │ ├── genomes
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| │ │ ├── hg19
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| │ │ │ ├── hg19_chr1.json
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| │ │ └── hg38
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| │ │ ├── hg38_chr1.json
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| │ ├── remap
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| │ │ ├── reMap2022.bb
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| │ │ ├── reMap2022.bed
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| │ │ ├── remap2022_all_macs2_hg38_v1_0.bed.gz
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| │ │ └── remap2022_crm_macs2_hg38_v1_0.bed
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| │ └── tfclust
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| │ ├── encRegTfbsClusteredWithCells.hg19.bed
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| │ ├── encRegTfbsClusteredWithCells.hg38.bed
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| │ └── encRegTfbsClustered_data
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| │ ├── hg19
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| │ │ ├── hg19_encRegTfbsClustered_chr1.json
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| │ └── hg38
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| │ ├── hg38_encRegTfbsClustered_chr1.json
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| ├── environment.yaml
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| ├── setup.py
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| └── tree_output.txt
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| ```
|
| 20 directories, 3089 files
|
|
|
| In `data_files` subfolders, only representative files for certain chromosomes are shown. In reality, any file that contains the substring "_chr" exists for every chromosome in that genome. Genome hg38 has 711 chromosomes. Genome hg19 has 298 chromosomes. To reconstruct a full directory structure, run the following from `DPACMAN`
|
|
|
| ```
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| tree -I '__pycache__|*.egg-info|*.git' > tree.txt
|
| ``` |
