Sijie Chen
Sijie Chen
to my knowledge, there are. such as sergio, etc
 I got this result after integrating smart-seq and 10x data of heart cells, can you tell me what parameters could be tuned to avoid this? before integration  codes:...
 Dear authors, thanks for you nice tool. I met a problem when integrating 6 samples. The loss did not drop but increased in the second iteration, and then converged...
### Prerequisites + [ ] Have you read [Feedback](https://guangchuangyu.github.io/clusterprofiler/#feedback) and follow the [guide](https://guangchuangyu.github.io/2016/07/how-to-bug-author/)? * [x] make sure your are using the latest release version * [x] read the [documents](https://guangchuangyu.github.io/clusterprofiler/documentation/) *...
Dear authors, I tried `'full reg'/ 'full eff'` modes in the `dyn.vf.rank_jacobian_genes()` function ``` full_reg_rank = dyn.vf.rank_jacobian_genes(abm2, groups='ann0608', mode="full reg", abs=False, output_values=True, return_df=True) full_eff_rank = dyn.vf.rank_jacobian_genes(abm2, groups='ann0608', mode='full eff', abs=False,...
Changes: 1. add **kwargs for the leiden(), louvain(), infomap() function calls in dyn.vf.cluster_field(), otherwise the function can only use default resolution settings 2. add a `resolution` parameter explicitly so users...
it seems that the current implementation of curvature() and acceleration() only insert a new layer when `basis=pca` I calculated the acceleration using umap and ran the rank test ``` dyn.vf.acceleration(adata,...
Dear developers, In Seurat's differentially expressed gene analysis function FindMakers(), there are "ident.1" "ident.2" parameters specifying group 1 vs group2. With these settings, users could flexibly compare customized two groups'...
The document says that by specifying 'group' it enable estimating group-specific kinetics parameters. Is it an implementation similar to the scvelo "Differential Kinetics" (https://scvelo.readthedocs.io/DifferentialKinetics/)? If yes, should I run similar...