TolgaDuz
TolgaDuz
Hi, i want to benchmark a snakemake-pipeline of mine. In snakemake one specifies a higher rule, called rule all, which must be achieved by smaler rules. after finishing rule all,...
I generated my embedding using Seurat, utilizing the raw count matrix rather than the spliced matrix. Following your instructions to project velocities onto this UMAP embedding, the process involves recalculating...
Hi @kstreet13, After using slingshot I get 5 different lineages. My dataset is integrated between two conditions. And I am interested in the genes that differ between those 2 conditions...
Hi together, When I count MXE events and run brie quant on it, I get a file where the chromosmecoordinates are listed (format: chr6:10749202:10749268:+@chr6:10749622:10749698:+@chr6:10755142:10755232:+@chr6:10770077:10770204:+ 24905) and p values etc. But...
Hi @huangyh09, thanks for this amazing tool! I n the outputfile (clusters.tsv), I can see two columns for p_values. One is called p_value and one is called condition_pval. What is...
Hi @sqjin, When I run the following code, I see that the communication probs between the conditions are not scaled. So I think this doesnt make it legit to compare...
Hi @sqjin, Thank you for the great tool! However, I'm experiencing a strange bug that doesn't appear in your tutorial. When I compare two conditions, the color coding and the...
Hello together, Due to the significant increase in the popularity of the stereo-seq platform, I highly recommend implementing wrapper functions for this type of analysis. I am currently having some...
Hi @WPZgithub , I always get an cuda out of error warning. The code doesnt work on my gpu or CPU. For the gpu I get the error message from...
Hi, I receive following error message after executing: %%time cefcon_results_dict = {} for li, data_li in data.items(): # We suggest setting up multiple repeats to minimize the randomness of the...