Comments (3)
Dear user,
in order to help you with your requests, I'll require additional information:
- How did you generate your list of target genes? Are those putative target genes of ligands (based on NicheNet predictions)?
- Is your data bulk-RNA seq or sc?
Unfortunately, we do not provide enrichment procedures based on target genes or predicted ligands in our package yet.
from nichenetr.
Thanks for your reply,
My data is single nucleus dataset. I followed the sender-focused approach. And the code I used to generate the target genes was:
active_ligand_target_links_df = best_upstream_ligands %>% lapply(get_weighted_ligand_target_links, geneset = geneset_oi, ligand_target_matrix = ligand_target_matrix, n = 200) %>% bind_rows() %>% drop_na()
active_ligand_target_links = prepare_ligand_target_visualization(ligand_target_df = active_ligand_target_links_df, ligand_target_matrix = ligand_target_matrix, cutoff = 0.33)
Moreover, if there is no function for enrichment analysis do you recommend any way to do so out of nichenetr (as you had one case in tutorial that target genes are the genes of a specific pathway)?
I appreciate your help on this!
Paria
from nichenetr.
Dear Paria,
In this case, I suggest utilising an over-representation analysis approach (enrichment procedures based on Fisher's exact test / hypergeometric distribution). This kind of approach requires the definition of a gene universe, which is the set of all the possible genes that might have been chosen as "interesting ones" or "not interesting ones" (e.g. in differential expression analysis, the former genes are those "differentially expressed" and the latter ones are "not differentially expressed").
In your case, your universe set is composed of all the target genes described in the ligand-target matrix.
To perform the analysis, you can use TopGO since it conveniently allows you to adjust for the gene universe. This package also supports enrichment procedures that leverage limitations that could arise if you use hierarchical structured annotations, such as GO-terms (e.g. parent-child terms relationships and information redundancy. Please, refer to Alexa 2006 for more info). I can not help suggesting specific sources for pathway annotations, since their quality might be subjective.
Best regards,
Daniele
from nichenetr.
Related Issues (20)
- Identifying bonafide ligand-receptor pairs in the updated ligand-receptor database (V2)
- SeuratV5 HOT 4
- Error finding log fold change information of ligands from sender cells (Seurat V5 object) HOT 6
- How exactly the ligand activity were calculate? HOT 1
- I cannot run the "get_weighted_ligand_receptor_links" and "prepare_ligand_receptor_visualization" while I have nichnetr installed HOT 2
- Preferable metric to infer cell-to-cell communication HOT 1
- what is ligand_tf_matrix for?? HOT 1
- `get_exprs_avg` changes underscore to hyphen in cell type names
- How to choose the best ligand to continue analysis with the potential ligand?
- cannot complete assign_ligands_to_celltype HOT 2
- missing function for circos plot visualization HOT 2
- I can't install nichenet HOT 1
- Condition_colname is not used for subsetting in nichenet_seuratobj_aggregate HOT 2
- `make_line_plot` bugs
- `assign_ligands_to_celltype` bug when there are no general ligands
- Error in `generate_info_tables`
- Warning message in `predict_ligand_activities`
- `generate_prioritization_tables` warnings and documentation
- Error when passing the recorrect_umi argument in get_lfc_celltype
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from nichenetr.