D2 is a fast and accurate tool for computing DNA Density and Distance to periphrery (DisTP). In our paper, we show that the DNA density and DisTP are highly correlated with nuclear activities. For detailed tutorial, please visit wiki.
paper.
D2 was tested on Python v3.9.1, with the following basic requirements:
- NumPy (tested on v1.20.2)
- SciPy (tested on v1.6.2)
- Pandas (tested on v1.2.4)
- Seaborn (tested on v0.11.1)
- Matplotlib (tested on v3.3.4)
D2 is a user-friendly scripts, which takes 3dg files and an index file as input, and outputs bed-like file storing the DNA density and DisTP.
Besides, we provided here the scripts for computing the enrichments of genetic markers, including the construction of density-DisTP matrix and calculation of enrichments. In order to achieve it, users should apply the genetic markers data of same reference genome.
Below is a typicle workflow using the test_data.
D2.py D2 and D2.py D2s compute the DNA density and DisTP. The resulted DNA and DisTP are stored in bed-like format file.
cd PATH/WHERE/D2/
mkdir -p test_data/results
python D2.py D2s ./test_data/dg_files/ ./test_data/hg19_diplo_20k.window.bed ./test_data/results/
D2.py sta gives the density and DisTP ranges, and a scatter plot as below.
D2.py map puts the bins on density-DisTP matrix, and stores the probability of genomic bins appearing at matrix bins (states).
D2.py ave computes the mean and standard deviation (SD) of density and DisTP.
python D2.py sta ./test_data/results/den_dtp/ ./test_data/hg19_diplo_20k.window.bed ./test_data/results/den_dtp_scatter.pdf
python D2.py map ./test_data/results/den_dtp/ ./test_data/hg19_diplo_20k.window.bed ./test_data/gm12878_histmap.txt
python D2.py ave ./test_data/results/gm12878_histmap.txt ./test_data/results/gm12878_ave.txt
D2.py marks indexes and concatenates the markers. D2.py enrich plotted the enrichments of markers individually. D2.py hiera ranks the matrix bins (states) by hierarchy cluster.
python D2.py marks test_data/marks/ test_data/hg19_diplo_20k.window.bed test_mark.mark.txt
mkdir test_data/results/enrich_pats
python D2.py enrich ./test_data/results/gm12878_histmap.txt ./test_data/results/gm12878_value_idx.txt ./test_data/results/enrich_pats/gm12878
mkdir test_data/results/hiera
python D2.py hiera ./test_data/results/gm12878_histmap.txt ./test_data/results/gm12878_value_idx.txt ./test_data/results/hiera/gm12878
Markers Enrichments Results: gm12878_1-Active-Promoter_histplot.pdf gm12878_13-Heterochrom_histplot.pdf
Hierarchy cluster Results: test_hiera_value_hierarchy.pdf test_hiera_hierarchy_hist.pdf
D2.py gene computed the fold changes of selected genomic regions (e.g., active genes) on D2 plot.
D2.py act computed the activation index.
python D2.py act ./test_data/results/gm12878_histmap.txt ./test_data/results/gm12878_act_index.txt
D2 is free for non-commercial use by academic, government, and non-profit/not-for-profit institutions. A commercial version of the software is available and licensed through Xi’an Jiaotong University. For more information, please contact with Yizhuo che (cyz0315@stu.xjtu.edu.cn) or Kai Ye (kaiye@xjtu.edu.cn).