Guido Hooiveld
Guido Hooiveld
Hi, First of all I don't know whether this is an `ggraph` or (under the hood a) `ggplot2` issue (or a problem simply caused by me), but since I experienced...
I tried but it didn't work, so therefore I explicitly would like to ask: is it possible to use `compareCluster` with `gseKEGG `(or the generic `GSEA` function), analogous to the...
Hi, I just saw your publication in [BMC Bioinformatics](https://doi.org/10.1186/s12859-021-04461-5) on `GeneTonic`, and I would like to say thanks for developing such nice project! I am playing now with the sample...
Hi, I don't know whether I should ask here, or at the maintainer of `fgsea` (@assaron), but after analyzing the example DOSE dataset using the GSEA algorithm implemented in either...
Hi, For further fine-tuning of the layout (because of overlapping nodes/labels) I would like to export the underlying networks generated by the `cnetplot` and `emapplot` functions for further processing in...
Hi Alex, A (reproducible) issue ("GSEA hangs") was posted on the `clusterProfiler` GitHub. See: https://github.com/YuLab-SMU/clusterProfiler/issues/659#issuecomment-2027820878, and posts below that one. Since `clusterProfiler` uses under the hood `fgsea` for gene set...
Hi Guangchuang, Maybe something to add/link to in your book: https://support.bioconductor.org/p/p134523/#p134554 ? It links to some example code on how to use `clusterProfiler` for analysis of proteomics datasets that use...
@GuangchuangYu , @huerqiang At the Bioconductor support forum an issue/error was reported regarding the function `buildGOmap`: https://support.bioconductor.org/p/9156358/ I had a quick look at it, and it seems this is because...
Hi, This may be a naive question, since I know `pcaExplorer` has been designed for RNA-seq data, but I am wondering...: would there be an easy way to use` pcaExplorer`...
Hi Johannes, I am trying to generate a mouse `EnsDb` for release 105, but unfortunately it doesn't work... I *think* this has to do with the library `ensembldb`, but I...