Lucille Delisle

I remember at one point I tried to make it work but I do not remember where I stopped: https://github.com/lldelisle/HiCBrowser/tree/update

I would also be in favour of a rescucitation/adaptation of HiCBrowser. In fact HiCBrowser is using a part of HiCExplorer which has slightly detached (pyGenomeTracks), we had in project to...

Hi, I think the issue is that the software consider that the interval: `chr1 710000 720000` both match to the bin `chr1 710000 720000` and the bin `chr1 720000 730000`,...

@joachimwolff The issue is here: https://github.com/deeptools/HiCExplorer/blob/20be92139dcfc6b4b215926b7fd8f4c7f6f48165/hicexplorer/hicConvertFormat.py#L210-L213 I think you were not expecting to find 2 bins for a region and you may consider using end-1.

Hi, Sorry for the late answer. @CocoMlle @Nadolina do you still have this issue? If yes, please explain how you installed HiCExplorer. Copy paste the full log of error you...

I managed using: ``` conda create -n testR3 python=2.7 r-base=3.6 r-terra=1.2 bioconductor-rhdf5=2.30 r-usethis=2.0.1 r-biocmanager r-dosnow r-plot3d r-ggplot2 r-umap r-gridextra pybedtools conda activate testR3 pip install snaptools R install.packages("devtools", repos =...

I think you could add somewhere the link to the protocol: https://dx.doi.org/10.17504/protocols.io.zcpf2vn

You are welcome. Maybe you can add me as 'editing author'. Have you thought about HOMER (findMotifsGenome) for motif detection?

I don't know. In my lab we use it. It is already in usegalaxy.eu.

Hi @hexylena and @heylf, If I am not wrong. For the moment these slides are just copy paste from ATAC-seq.