André F. Rendeiro

icon indicating a website link https://andre-rendeiro.com icon indicating an email [email protected]

icon company CeMM - Research Center for Molecular Medicine icon location Vienna, Austria icon location Principal Investigator at CeMM - Research Center for Molecular Medicine, Vienna Austria; Leading @rendeirolab

Results 11 comments of André F. Rendeiro

load .bashrc configuration on terminus_open

In Ubuntu 22.04 I had to source my `~/.bashrc` file from `~/.profile`.

Release for python 3.10

Just tested on 3.10 after changing the `python_requires` in `setup.py` for deepcell-toolbox and deepcell-tf.

Incompatibility with Python 3.9x or Numpy versions.

Can confirm the same using Python3.9 and numpy==1.19.5, solved with numpy upgrade to 1.21.0.

Fixed setup file

Also fixes install issue in Python 3.11. Thanks a lot!

error in plotter: `ctypes.ArgumentError: argument 2: TypeError: wrong type`

Same issue here with Python 3.10 and 3.11

Unable to run dca with mode='denoise'. 'ValueError: setting an array element with a sequence.'

@fangfang0906 I experience the same: the problem seems specific to sparse input.

ATAC-seq pipeline exit if no mitochondrial reads are duplicated

Yes, I am maintaining it. But you can always try [pepatac](https://github.com/databio/pepatac).

Sample name uniqueness?

Yeah, I think the current implementation is good. It actually happens to me often in big projects that I end up with duplicate sample names but this is always by...

separation of looper-specific config attributes

Yep, makes sense those would be under `looper`. I think that as you point out, a pep should not necessarily be restricted in what sections it have and could allow...

Referencing python package files as paths in PEP

> It seems like geofetch is one of a kind as pipelines go, and we do not distribute pipelines as software packages. These are kind of ever changing codebases. Are...