Guangchuang Yu

We use the `showCategory` parameter to specify which terms are used in the plot and the source codes used to do the subsetting are similar in several functions in the...

After network module identification (by WGCNA), the modules can be characterized by functional annotation (e.g., GO, KEGG). The `compareCluster()` function provided in the `clusterProfiler` package can be employed to perform...

customize upset plot with aplot

6

We can consider the upset plot as a composite plot, where each part can be drawn in the way that suits your needs, and then pieced together using `aplot`. For...

reproduce a funkyheatmap using aplot

8

using `ggplot2` to plot columns and using `aplot` to create a composite plot. Please reproduce the `funkheatmap` demonstrated in the [README](https://github.com/funkyheatmap/funkyheatmap).

see .

write an R function to parse eggNOG annotation

5

eggNOG can functionally annotate a large number of non-model organisms. Once we are able to parse the output of eggNOG, we can easily combine it for analysis with GOSemSim and...

GO enrichment analysis on proteomics data

1

Most enrichment analysis tools are designed at the gene level and only support gene IDs. The first step to performing GO analysis for proteomics data is to convert protein IDs...


As I proposed in and the feature requested in , it is nice to have metadata for reference.

add sub-category information of the KEGG pathways

6

KEGG can be divided into 7 categories, see . It is easy to incorporate this information in the `enrichKEGG()` and `gseaKEGG()` results, so that we can use this information to...