ShengyuLi
ShengyuLi
Hello zcaiwei, thank you for reaching out! Is it possible for you to try to decrease the parameter min_mass when plotting? If you have any other questions, please feel free...
Hello, Thank you for reaching out. When running the prediction, we assume the batch effect is already corrected. From my own experience, you can observe both ’the embedding space‘ and...
Hello, Thank you for reaching out. Your question looks related to [this question](https://stackoverflow.com/questions/75853863/install-pytorch-version-1-0-0-using-pip-or-cuda-in-2023). I tried in my conda environment and I was able to install torch==1.10.0. To get around it...
Hello, could you change it to 0 and see what happens? Thank you!
Hello, Thank you for reaching out. We did not specify the device or benchmark the resource usage in GPU in our algorithm. We use pytorch lighting in the algorithm so...
Hello, Thank you for reaching out. The [to_dynamo](https://guangyuwanglab2021.github.io/cellDancer_website/celldancer.to_dynamo.html) function might be helpful for you to transfer the dataframe to data. Then you can extract the velocity matrix from the adata....
Hello, Thank you for reaching out. The [preprocessing](https://guangyuwanglab2021.github.io/cellDancer_website/data_preprocessing.html#preprocessing ) example allows you to obtain the top 2000 genes. You can also specify your top n genes. For finding genes of...
Hello zcaiwei, thank you for reaching out! If you would like to have the velocity1 and velocity2 for all cells, speed_up parameter could be set to None. This will consume...
Hello, Thank you for reaching out. Can we have the information on the error you met? The [installation](https://guangyuwanglab2021.github.io/cellDancer_website/notebooks/installation.html) page might also be helpful. Best, Shengyu
Hello xiao00su, thank you for reaching out. We manually searched the boost genes and the branching genes. This question is also related to [this issue](https://github.com/GuangyuWangLab2021/cellDancer/issues/8). If you have any other...