pyDNase
pyDNase copied to clipboard
jpiper
Python module for the easy handling and analysis of DNase-seq data
Hello, Recently I use pyDNase to deal with my ATAC-seq data. I encounter a question like below，and I used python 3.6 version. I don't know how to handle this. Could...
Hello, Is there a plan to update pyDNAse to an updated version of matplotlib? `ERROR: pydnase 0.3.0 has requirement matplotlib
Hi, This might be same type of question as #29 or #37. I have ATAC seq data and whenever I run wellington on my data, I get "waiting on last...
Hello, I recently attempted differential footprinting for the first time with wellington_bootstrap.py. After running the output files were completely empty. There were no errors raised during the run. Is this...
Hi! Recently I'm using pyDNase to analyze some ATAC-seq data. It's a very convinient tool! However, I noticed that in the original ATAC-seq paper it said: "all reads aligning to...
https://github.com/jpiper/pyDNase/blob/master/pyDNase/__init__.py#L349 requires strandedness in the bed file. It would be nice for `pyDNase.GenomicIntervalSet` not to break with unstranded lines from a bed file
I apologize if this has been asked, but I haven't seen this same question. When running wellington_footprints.py I get an error stating: line 83 print("track type=wiggle=_0", file=wigout) With a carrot...
Hi! Whenever I run wellington on my data, I get "waiting on last 80 threads." as the last output When the process eventually ends, the footprint output file is empty....
