Zhuoqing Fang
Zhuoqing Fang
Thanks for the comparsion, too. Yeah. It's my bad. I should notice the weird thing more earlier. I thought the previously result was caused by the approximate method I've implememented....
in the previous version, the final output results are sorted by FDR. Now are sorted by the absolute value of NES, which will make the sorting order more deterministic. The...
The prerank expected a pre-sorted values (descending order) and gene order matters ! Same values input won't be a problem. e.g you could set weight_score_type to 0, and every value...
Hi @Gin-Wang , 1. Would you show me the parameters when you ran GSEApy and GSEAv4.0 ? It shouldn't be such difference. One more thing is that GSEAv4.0 and GSEApy...
What's your command for GSEApy? GSEApy use permutation type `gene_set` and ranking metric with `log2_ratio_of_classes` by default. 1. for png question, just save your figure in pdf format, and then...
It's very easy to do this, if you know python. For command line, split them into 3 matrix.
This could be done. However, if our ranked gene list are smaller than 15, prerank analysis is still make sense to us? @michaelpierrelee
`min_size` and `max_size` are used for filtering how many gene members of a pathway (gene set) should overlap with your ranked list. A ranked list containing all expressed genes in...
Yes. You need Rust compiler. See #161 install rust first ```shell mamba install rust ``` or install mannually
Now, for py >=3.7, you could use ``` conda install -c bioconda gseapy ``` So you don't need to install rust compiler by yourself.