Chris Doan

Hello all, I try to install snakemade by follow this tutorial: [snakemake tutorial](https://snakemake.readthedocs.io/en/stable/tutorial/setup.html#step-1-installing-mambaforge) When I run: `snakemake --help` I got this error: -bash: /home/doanc2/mambaforge/envs/snakemake-tutorial/bin/snakemake: /home/doanc2/mambaforge/envs/snakemake-tutorial/bin/python3.8: bad interpreter: Permission denied Would...

Help with Kernal dead

9

Hi team, Would you please suggest what cause the kernal dead error? Thank you so much! This cell ran for about 2 hours and then I got the error kernal...

Help with AssertionError: Database "{fname}" doesn't exist.

2

Hi all, I downloaded 3 files required but still got fname doesn't exist error. Would you please have a look? Thank you so much! **Describe the bug** AssertionError: Database "{fname}"...

Error with plot_topic

4

Hi all, I try to run the tutorial but got this error. Would you have a suggestion? **To Reproduce** plot_topic(cistopic_obj, reduction_name = 'UMAP', num_columns = 4) **Error output** ```python ValueError...

Hi team, Would you please suggest what cause the kernal dead error? Thank you so much! This cell ran for about 2 hours and then I got the error kernal...

Data to follow along

1

Hello all, I try to follow along with the analysis in this workshop. However, when I click to download data, I am not sure I got the correct files because...

Error when install CellO

11

Hello all, I run: `pip install pygraphviz leidenalg scanpy cello-classify` And this was what I got: pygraphviz/graphviz_wrap.c:2711:10: fatal error: 'graphviz/cgraph.h' file not found #include "graphviz/cgraph.h" ^~~~~~~~~~~~~~~~~~~ 1 error generated. error:...

Hi Fabian, I follow the vignette and run: `run_atac("ChrAccR_analysis", "bamFilenameFull", sampleAnnot, genome="hg38", sampleIdCol="sampleId", regionSets=regionSetList)` After a long run time, I got this: Loading required namespace: DESeq2 converting counts to integer...

Hi Fabian, I have an error message when run: `run_atac("ChrAccR_analysis", "bamFilenameFull", sampleAnnot, genome="hg38", sampleIdCol="sampleId", regionSets=regionSetList)` Error in (function (cond) : error in evaluating the argument 'x' in selecting a method...

Association between pathway score of two pathways

2

Hi team, After run gsva, I have pathway score. Then I try to find association between pathways of interested using cor.test(). However, when I pick two random pathways to find...