scarches
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theislab
Reference mapping for single-cell genomics
I tried to install `scarches` in a conda environment I created like this: `conda create -c conda-forge -n sca python=3.8 numpy gdown scanpy pytorch pandas matplotlib seaborn pillow scipy` After...
Hello, If I use cells from normal sample as reference, can I use scarches to annotate the cancer cells in the tumor sample ? Thanks !!!
Hi, Are there any recommendations on how to mismatch/process query datasets where not all HVGs of the reference are within the query? Should we be zero padding missing data?
I'm trying to reproduce the semi-supervised pipeline in here [https://scarches.readthedocs.io/en/latest/scanvi_surgery_pipeline.html], but the pipeline is failing when trying to build the model using the reference dataset: >>> sca.models.SCANVI.setup_anndata(source_adata, batch_key=condition_key, labels_key=cell_type_key) Traceback...
Hi, I am going through the scArches paper. I have a couple of doubts after reading it. - In the fine tuning network, what do the adaptor neurons have? Do...
Hi, when I want to implement CVAE, I set use_mmd=False and beta = 0 in Class TRVAE. Is that right? Is there anything else that needs to be changed when...
Would it be possible to publish this on Bioconda in addition to PyPi? I'm happy to help write and submit a recipe.
I have a model trained on ref_data with cell type labels vae = sca.models.SCANVI( ref_data, "Unknown", n_layers=2, encode_covariates=True, deeply_inject_covariates=False, use_layer_norm="both", use_batch_norm="none" # use_cuda=True ) vae.train( max_epochs= 400, use_gpu= False )...
I cloned the repo and ran python3 setup.py install in the scarches directory, but I run into this error: Installed /usr/local/lib/python3.8/dist-packages/scArches-0.5.4-py3.8.egg Processing dependencies for scArches==0.5.4 error: rich 12.5.1 is installed...
