wajm

Hi, @Alexander230! Thanks for your kind response. Here, "Working with sample files" section shows example files are txt files. https://immunarch.com/articles/v2_data.html I thought I could make same format with my BD...

@Alexander230 Ok, I'll test it. An attached file is BD Rhapsody VDJ output csv file. Please check it. Thanks a lot. JungMo

for using seurat object, STREAM had suggested loomR conversion in seurat. however now loomR using seurat-disk, all setting is change.

Okay, I've tried this. and working like previous #100 setting. but I'm not sure this is correct or not. Please check this. ### patient object is subset of original my...

I'm realized an issue. in STREAM: adata = ad.read_h5ad("patient.h5ad") st.set_workdir(adata,'result') st.add_metadata(adata,file_name='metadata.txt') adata.obsm['top_pcs'] = adata.obsm['X_pca'] adata.obsm['X_dr'] = adata.obsm['X_umap'] adata.obsm['X_vis_umap'] = adata.obsm['X_umap'] For my integration Seurat object, upper code in STREAM was...

> Hi, the setting looks all right to me. It seems the same as the code you shared previously though. I am not sure what the problem here is. hmmm....

> AnnData object with n_obs × n_vars = 11826 × 2000 obs: 'label', 'label_color' var: 'features' uns: 'workdir', 'label_color' obsm: 'X_pca', 'X_umap', 'top_pcs', 'X_dr', 'X_vis_umap' varm: 'PCs' in my data,...

I have also similar issue, --------------------------------------------------------------------------- ModuleNotFoundError Traceback (most recent call last) in () 1 import anndata as ad ----> 2 import stream as st /Users/wajm/.pyenv/versions/anaconda3-2020.07/envs/env_stream/lib/python3.6/site-packages/stream/__init__.py in () ----> 1...

I've found solution. under env, update tzlocal and rpy2.

thank you for kind information. btw, my seurat integration object make some problem. after making loom format, adata.obsm['top_pcs'] = adata.obsm['pca_cell_embeddings'] adata.obsm['X_dr'] = adata.obsm['umap_cell_embeddings'] adata.obsm['X_vis_umap'] = adata.obsm['umap_cell_embeddings'][:,:2] these are not working....