gene co-expression networks
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 2.6k
- Forks
- 779
- Avg merge
- 1d 4h
- Merged PRs (30d)
- 27
Description
We are very impressed with the scalability of scanpy. We are interested in performing gene co-expression clustering on large single-cell RNAseq datasets. This typically involves calculating pairwise correlations between genes, then using these correlations as distance metrics for hierarchical and k-means clustering. Does scanpy already support these kinds of analyses?
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
No files, tests, or entry points are identified in the issue. Begin by checking whether scanpy currently supports pairwise gene correlations and hierarchical or k-means clustering for large single-cell RNA-seq datasets; document what is already available and define the missing behavior needed to consider the request addressed.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, data, machine-learning
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100