createKEGGdb
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YuLab-SMU
Create KEGG.db Package
作者您好 我从`http://rest.kegg.jp/list/organism`获取了所有所有物种名称后，使用createKEGGdb包进行全体物种的KEGG数据库构建 ```R create_kegg_db(keggOrganism) ``` 结果在下载到第475个物种时，发生错误如下： ```R Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/vps"... Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/vcrb"... Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/vve"... Error in content[, 1] : 下标出界 ``` 请问如何处理呢？
Something wrong with download KEGG dataset. Here I correrted this part. #options(clusterProfiler.download.method = "wget") enrichKEGG(de,pvalueCutoff=0.01,use_internal_data = F) --> No gene can be mapped.... --> Expected input gene ID: --> return...
Dear authors, please pay attention to this issue:  ``` r$> clusterProfiler:::kegg_list("all") Reading KEGG annotation online: "https://rest.kegg.jp/list/all"... fail to download KEGG data... NULL Warning message: In download.file(url, method = method,...
Hello, Thanks for this useful package! I have some questions on what exactly is stored in the resulting `KEGG.db`, and how that relates to the options of `clusterProfiler::enrichKEGG`. `enrichKEGG` has...
Hi, I want to try the method to get the latest information about zea mays. But when I type "remotes::install_github("YuLab-SMU/createKEGGdb") " on RStudio, the program reported an error: Downloading GitHub...
I want to try the method to get the latest information about E.coli.But when I type remotes::install_github("YuLab-SMU/createKEGGdb") on RStudio,the program reported an error. > remotes::install_github("YuLab-SMU/createKEGGdb") Downloading GitHub repo YuLab-SMU/createKEGGdb@master Skipping...
I'd follow your package, but `backgroud number` of KEGG is not consistent with Online for mouse. KEGG.db is 7650 but online is 8656.
