Ming Tang

Hi, how did you get the gene activity score? Did you use the enhanced model or simple model? If you get the activity score from running the MAESTRO snakemake pipeline,...

how did you get the gene_peak matrix? you are right, for every peak, the max weight should be 1.

We have not done anything to support other species. Yes, the LISA will only work for human and mouse data. We will consider supporting other species if there is a...

@baigal628 can you please ask @pengxin2019 for a list of genome annotation files so we can expose MAESTRO to accept them? we can then write a tutorial for other species....

@pengxin2019 we are much interested in supporting other species, if you can provide some example data that would be great. thx.

so -f BAMPE is preferred for paired-end ATAC-seq?

this worked for me after changing adata.obsm['X_vis_umap'] to adata.obsm['X_dr']. Thanks! also the docker version lacks loompy installation.

Thanks @huidongchen. ```python adata.obsm['X_dr'] = adata.obsm['umap_cell_embeddings'] adata.obsm['X_vis_umap'] = adata.obsm['umap_cell_embeddings'][:,:2] ``` `X_dr` is used for trajectory inference, `X_vis_umap` is for visualization right? I guessed from the names of the variables.

Hi Huidong, I went on to do marker detection at each leaf: ```python st.detect_leaf_markers(adata,cutoff_zscore=1.0,cutoff_pvalue=0.01, root='S3',n_jobs=4) ``` I got this error ``` --------------------------------------------------------------------------- ValueError Traceback (most recent call last) ~/anaconda3/envs/stream/lib/python3.6/site-packages/pandas/core/internals/managers.py in...

@huidongchen Thanks! this worked for me.