decoupler-py

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CytoSig resource providing incorrect data

2

**Describe the bug** It's unclear what the CytoSig resource is outputting. For example, ``` res = dc.get_resource('CytoSig') res ``` Provides a DataFrame with this info ![Screen Shot 2022-09-26 at 3...

adamgayoso

run_ora using adata as the input

2

**Describe the bug** Using adata as input, if there is an empty sample (i.e., expression of the cell/sample is 0 for all genes), there will be an error writing the...

biopzhang

Marsilea error in dc.plot_associations()

1

**Describe the bug** Hi, I'm following the tutorial for my own data and I get an error at the `dc.plot_associations()` step: `TypeError: ColormapRegistry.get_cmap() missing 1 required positional argument: 'cmap'` Is...

dnjst

This updates _pre for faster dataloading. I also changed `tqdm` to `tqdm.auto` so that it looks better in notebooks

Intron7

Dataloading

1

Within `_pre.extract` you don't support `layer` and `use_raw` is set to true by default. I would suggest to add support with `_get_obs_rep` from scanpy (it's small codeblock that you can...

Intron7

Warnings about annotations raised when running `dc.plot_targets`

1

**Describe the bug** While running codes as tutorial "pseudobulk functional analysis", the function `dc.plot_targets` raised dozens of warnings, namely `WARNING:matplotlib.text:posx and posy should be finite values`, and there isn't any...

Fantasque68

Error when running get_pseudobulk(): AttributeError: 'csr_matrix' object has no attribute 'A'

2

Hi! I'm running your tool on a jupyter notebook (python 3.12, macos) using an anndata generated with scanpy (1.10.1) I got this error message when running get_pseudobulk():  I solved...

raquelgarza

psbulk_counts are associated with top PCs

5

Hi, first of all thanks for the great documentation. I am running the pseudobulk analysis and I found the pseudobulk_counts to be signficantly associated with the top PC which thus...

singlecellfan

get_pseudobulk losing obs columns with NA values

1

Hi, It appears that `get_pseudobulk` loses `.obs` columns when they contain NAs, even when they are unique for each sample ID. Here's an example. ```python import pertpy import decoupler adata...

emdann

Python and R versions of package giving different results

1

Hi, I wanted to first and foremost express my appreciation for this fantastic package! I am trying to apply the TF activity inference functions on my 10X scRNA-seq data. For...

shaln