Dongze He

Hi, I use `pyranges` in my [function](https://github.com/COMBINE-lab/pyroe/blob/main/src/pyroe/make_splici_txome.py). As this warning keeps showing when I run `pytest`, I sincerely hope you can fix it. Thank you. - Dongze

Great! Thanks so much! Here are the warnings I got. Hope it will help you locate the places to change. ``` /home/zaza/miniconda3/envs/pyroe/lib/python3.7/site-packages/pyranges/methods/merge.py:71: DeprecationWarning: `np.long` is a deprecated alias for `np.compat.long`....

Hi @endrebak, There were errors reported by gcc((Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0) when I install the packages you mentioned. If possible, could you also update them in conda? thanks! ``` $ pip...

Thanks for your quick reply! One more strange behavior I noticed is that after running introns() with `nb_cpu` > 1, every call of the system shell command via `subprocess` functions,...

I am using luigi and here is my command: ``` luigi --local-scheduler --module qanta.pipeline.buzzer ``` The problem is in the qanta/pipeline/buzzer.py, it imports `test.py` and 'constants.py' from `qanta/buzzer/` folder, while...

Hi all, Given the `new_gtf.fixed.gtf` file from the `rg` command above, the `clean_gtf.gtf` file @rob-p uploaded is from the following process: If using the development branch of the repository (clone...

According to its [user guide](https://cdn.10xgenomics.com/image/upload/v1694504965/support-documents/CG000691_ChromiumFixedRNAProfiling_SingleplexedSamples_UserGuide_Rev_A.pdf) from 10X, I don't think there is any difference between processing this kind of data with processing 10X Chromium v3.

Hi all, I totally agree with what @rob-p said. One thing to add: If you have an expected number of cells in your mind, you can also try to run...

Is there any update?

Hi @endrebak, I am still getting the warning using the latest version of pyranges (v 0.0.120). I suggest specifying the required version of pandas in the setup.py as currently there...