All Questions
Tagged with single-cell python
5 questions
2
votes
0
answers
217
views
How to make a UMAP for single cell data and color cells by average expression of a list of genes in scanpy?
I would like to make a UMAP where the cells are colored by the average expression of the bulk signature genes but I am not confident that I did it correctly. I would like to use scanpy for it.
I did ...
- 135
2
votes
0
answers
202
views
pyScenic CLI for ctx is giving error: Not a single module loaded
Hi I ran pyScenic's ctx via the command in command prompt:
...
- 21
3
votes
0
answers
319
views
How to concatenate 2 `mdata` of `muon` package?
I used muon(https://github.com/scverse/muon) for single cell Multimodal omics analysis.
How to concatenate 2 mdata from ...
- 141
1
vote
1
answer
110
views
Segment cell organelles with pixellib
I've got some images of cell organelles and I really want to avoid labeling them by hand. The images all look something like the image below. Is there already an existing model specifially for cells? ...
1
vote
1
answer
68
views
semantic similarity measurement for cell line ontologies
I have a set of cell line pairs and I want to know to what extent the pairs are similar based on their ontologies.
The problem I have is that I have found a Python library called Fastsemsim, but it ...
- 111