Sirin24

Can not detect a neighborhood graph, will construct one before the over-clustering

1

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...

why some of the atlases on cellxgene do not have PCA in them. How can we use them to annotate our sample? as most tools require the presence of PCA...

Hello, I want to be able to have an html file or pdf file from .ipynb or .py file. I use slurm on a server what I did : I...

reference mapping

3

i am following https://docs.scvi-tools.org/en/stable/tutorials/notebooks/scrna/scarches_scvi_tools.html#reference-mapping-with-scanvi >>> import os >>> import tempfile >>> import anndata >>> import matplotlib.pyplot as plt >>> import numpy as np >>> import pandas as pd >>> import...

Hello, I have a question regarding how to run velocyto. if i plan to take raw counts from veloctyo and use some matrix correction tools such as soupX, do I...

BPCells to h5ad

3

Thank you for this great tool. I have finished integrating and annotating my data which could not have been done without this tool. Now I need to convert the object...

harmony or not

1

hello, I want to ask if i downloaded an annotated reference already batch corrected then annotated ( comes with counts only and the cell labels) and i will be using...

compare between different conditions

1

Hello, i want to compare between 3 different conditions. do i run pyscenic on each disease and its control only ? or on a subset of the whole object. I...

Hi, I ran pyscenic on a loom file that contains diseased and healthy cells (2 conditions) and I plotted a heatmap of the auc scores and it seems whenever i...