Ignacio L. Ibarra

Dear @marakeby, Thanks for developing and releasing PNET. I am trying to do exploratory analyses in some multimodal data using this framework. Labels are more than two, so I wonder...

During installation I found a conflict with the `decorator` package version that is installed. Namely, the default version conda installs gets into conflict because it gets in conflict with `...

Feature request - var_names/obs_names as fixed-sized types (integer or bytes)

12

Following issue #35, using integers in obs_names/var_names is allowed, yet slicing the objects is not possible after that. Could solutions for this particular exceptional case be discussed/added to the codebase?...

MPRA tutorial - testing r2 with CPU not agreeing with GPUs.

1

Thank you for the development of this package, I am able to reproduce the tutorial results for MPRA (test R2) only when using GPUs. `2020-05-25 13:18:22,128 - test r2: 0.9223668070860704`...

Problems with scglue.models.integration_consistency in train.ipynb with few cells (~n=500).

1

If subsetting ~500 cells for both RNA and ATAC, in the training tutorial ```python rna = rna[rna.obs_names.isin(rna.obs_names[:500]),:].copy() atac = atac[atac.obs_names.isin(atac.obs_names[:500]),:].copy() print(rna.shape, atac.shape) ``` I get the following error (below) when...

matplotlib.tight_layout restricts matplotlib version to 3.5.2

3

Dear UpSetPlot team, On an issue related to matplotlib in this repository, I am asking whether this dependency limitation of matplotlib to version 3.5.2 can be considered and fixed to...

Following on this issue (closed, but I cannot find a solution). I am kindly requesting a requirements.txt file or similar to run the main examples of this code successfully. https://github.com/dmis-lab/hats/issues/5...

Retrieval of md5 IDs for files available on website.

1

Dear ChIP-atlas team, I am interested in the retrieval of md5sum IDs for website available files. This is relevant for tracking files in case of future changes to those files....

getting reads counts from bigWig file.

2

Dear ChIP-atlas team, Thank you for the dev and maintenance of this fantastic resource. I was wondering if more details can be given regarding the bigWig files provided e.g. for...

High RAM peak while loading h5ad.

1

Thanks you for dev of this package! We're using this package for loading the open problems h5ad file in a tutorial from the [best practices book](https://github.com/theislab/single-cell-best-practices/blob/grn/jupyter-book/mechanisms/regulons_rna_and_atac.ipynb) (70k cells, 130k features)....