rapids-single-cell-examples

rapids-single-cell-examples copied to clipboard

I am facing this error when i try to reproduce notebooks/hlca_lung_gpu_analysis-visualization.ipynb , ani ideas how to overcome this error? Had to reduce the data in order to fit in the...

animesh

csr_matrix with the .get method will return "Last value of index pointer should be less than the size of index and data arrays"

3

``` import scanpy as sc import anndata import time import os,wget import cudf import cupy as cp from cuml.decomposition import PCA from cuml.manifold import TSNE from cuml.cluster import KMeans from...

linmuchuiyang

Colab implementation

2

Thanks for creating the notebooks! I was interested in trying out the examples with an easy access to GPU. Are there plans to support Colab-friendly notebooks? I put up a...

saketkc

conda import environment not working

1

When I try creating a conda env from the provided yml file, I get an error report that ends with the following: File "C:\Users\tnnan\anaconda3\lib\site-packages\ruamel_yaml\scanner.py", line 651, in fetch_value raise ScannerError(...

tnnandi

rank_genes_groups fix

1

Dear all, I fixed the `rank_genes_groups` function. However I change quit a bit of the preprocessing e.g. masking from cupy to numpy. In the notebooks that I was able to...

Intron7

Hi, the rapids-single cell workflow is excellent! Do your team have any plans to write pyscenic into rapids in the future? Now pyscenic makes use of CPU and is slow...

Wulin-Tan

CUDARuntimeError in Notebooks

15

Hello everyone, I'm having trouble running the notebooks on our institutes server (64 Core Epyc and 2 Quadro RTX 6000), however when I'm at home running them on my personal...

Intron7

Nearest neighbors graph computation crashes

1

Hi, I am trying the hlca_lung_gpu notebook with my own data to test the dimensionality reduction on GPU. The notebook is running well (data loading, pca...) until the nearest neighbors...

manock

RAPIDS implementation of Scanpy rank_genes_groups appears incorrect

6

I tried running the RAPIDS implementation of rank_genes_groups alongside the Scanpy CPU implementation on the same data matrix, but I'm getting very different results. Here's my code for the GPU...

rmovva

Opening this issue for tracking purposes and linking https://github.com/rapidsai/cuml/issues/2597. At the time of writing this, the major effect of this bug has been on the `PCA` step and the `LogisticRegression`...

cjnolet