celltypist
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Teichlab
A tool for semi-automatic cell type classification
Dear Celltypist Team, Are the confidence scores of celltype predicted by different reference models comparable? whether I could choose the most suitable model to annotate new datasets by comparing the...
Hello : ) Im trying to run cell typist with my own model and in the step "Training data using SGD logistic regression" I get the following error: ``` OMP:...
Hello, I appreciate your work in making CellTypist available. I have been able to use the python API to assign predicted_labels and majority_voting types to our data but am getting...
📜 Retrieving model list from server https://celltypist.cog.sanger.ac.uk/models/models.json --------------------------------------------------------------------------- timeout Traceback (most recent call last) ~/.conda/envs/single_cell_v0.1/lib/python3.7/site-packages/urllib3/connectionpool.py in _make_request(self, conn, method, url, timeout, chunked, **httplib_request_kw) 381 try: --> 382 self._validate_conn(conn) 383 except...
Dear, In the description of the model it is not clear whether the model involves cells from both healthy and CD or just healthy? I am especially referring to 'Cells_Intestinal_Tract...
I ran celltypist on my data with a custom model and the output had the above column. I wanted to ask what does it exactly represent?
I would like to train cell typist on different data sets. Should I merge the 2 data sets and train the model once or train 2 models and do the...
Hi, I have been seeing the same timeout error message when trying to download models in both command line and python versions: import celltypist from celltypist import models models.download_models(model =...
This adds support for rapids-singlecell for the `over clustering` #110 . The results might differ a bit since rsc uses a brute-force knn approach and the leiden clustering is also...
sorry for the very basic questions but i was following this for a custom reference https://colab.research.google.com/github/Teichlab/celltypist/blob/main/docs/notebook/celltypist_tutorial_cv.ipynb#scrollTo=therapeutic-mixture 1) predictions = celltypist.annotate(adata, model = new_model, majority_voting = True) I received the following...
