cbravo

Bug in diffusion map plotting in 1.9.1?

3

- [ x] I have checked that this issue has not already been reported. - [ x] I have confirmed this bug exists on the latest version of scanpy. -...

I am interested in using LightLDA; however I am unable to find how to extract the topic word distribution after training the model (with fit_transform only the doc_topic distribution is...

[BUG] Removing Log and moving color bar in numerical metadata breaks metadata

1

Hi! When checking numerical metadata, using Log returns the correct plot:  When removing the Log tag also returns the correct plot:  However, when moving the bar all colors...

Would it be possible to interactively select a threshold for which we want the gene to be considered not expressed? For example, to show in grey/black all the cells that...

Not working with Loompy v3

3

Hi, The current loomR version does not seem to work with loompy v3. Are you planning to upgrade loomR to be compatible with it? Thanks! C

[BUG] Error downloading CPTAC-3 SNV data

1

Hi! I am unable to download the CPTAC-3 SNV data: - Code ``` query

Bug: Installation of MACS2 with pip in python 3.10

2

**Describe the bug** Installation with pip install macs2 in Python 3.10 fails, with a critical error complaining about the python version even though it is correct: ``` Collecting MACS2 Downloading...

Hi! I have noticed that when using the compare tab with a loom file with a lot of metadata the viewer gets stretched (see example below), which makes it a...

Self-loops in ce_cell_type_network_plot

1

Hi! Is there any way of plotting autoregulatory links (i.e. when ligand-receptor are produced by the same cell-type)? Thanks! Carmen

**Is your feature request related to a problem? Please describe.** Add custom colors for categorical variables in loom files (applicable to SCENIC+/pycisTopic) **Describe the solution you'd like** See Sara's notebook