Hi @tanlongzhi
Thanks for your powerful Dip-c tools. I am looking for a way to generate a 3D proximity map like the one you mentioned in your article.
A 3D proximity map—a matrix of fractions of cells where each pair of 20-kb particles are nearby in 3D (distance ≤ 3.0 radiiwas then generated by binarizing each single-cell matrix of pairwise 3D distances and averaging them, with “scripts/threshold_np_float.py” of the “dip-c” package (“scripts/threshold_np_float.py 3”).
And I did not find such scripts in the files. I guess it may be moved to somewhere else. Could you please tell me where it is? Thank you.
Also, I am trying to figure out the TADs in single cells and I saw TAD.py in this file. Is the output file of dip-c tad-l shows the exact region of TAD regions? And is there a way to visualize such a TAD result file? Any information or guidance is really appreciated. Thank you.
Hi @tanlongzhi Thanks for your powerful Dip-c tools. I am looking for a way to generate a 3D proximity map like the one you mentioned in your article.
And I did not find such scripts in the files. I guess it may be moved to somewhere else. Could you please tell me where it is? Thank you.
Also, I am trying to figure out the TADs in single cells and I saw TAD.py in this file. Is the output file of
dip-c tad-lshows the exact region of TAD regions? And is there a way to visualize such a TAD result file? Any information or guidance is really appreciated. Thank you.Yuchen