Huansheng Cao

no output with either test data or my own data

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I debugged and it seems to be an samtools problem, everything run fine till samtools kicks in. the test data would go through the whole process. I cannt seem to...

**Describe the bug** in the downloading process, the git close using https url did not work, but the ssh git worked (see extra note at bottom) in the installation process,...

**Describe the bug** A clear and concise description of what the bug is. **To Reproduce** from pycisTopic.iterative_peak_calling import get_consensus_peaks # Other param peak_half_width=250 path_to_blacklist="pycisTopic/blacklist/hg38-blacklist.v2.bed" # Get consensus peaks consensus_peaks =...

errors running full human multiome

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i need to reproduce these two analyses [full-multiome](https://www.github.com/pinellolab/dictys/blob/master/doc/tutorials/full-multiome): an extended version of the above tutorial with detailed usage. [full-skin](https://www.github.com/pinellolab/dictys/blob/master/doc/tutorials/full-skin): a short tutorial for the inference and analysis of dynamic networks...

it would be nice to provide the results with each step of the analysis. this would help with debugging greatly.

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**Is your feature request related to a problem? Please describe.** A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] **Describe the solution you'd...

pycisTopic label transfer failure

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**Describe the bug** Hi @SeppeDeWinter and others, the 'label transfer' step did not go through when i run scenicplus for pycisTopic, I followed the tutorial here: (https://pycistopic.readthedocs.io/en/latest/notebooks/human_cerebellum.html) I run scenicplus...