DOSE
DOSE copied to clipboard
YuLab-SMU
:mask: Disease Ontology Semantic and Enrichment analysis
I have edited setReadable and EXTID2NAME functions so they now they accept an additional parameter, "keyoutput", to call an alternative OrgDb output column holding gene names/symbols rather than enforcing the...
老师，我先把DOSE数据更新的一些东西做个PR，对gson的修改我将在另外的PR中进行。此次PR共涉及三个包：分别是DOSE、[DOyulab.db](https://github.com/huerqiang/DOyulab.db) 和 GOSemSim。 ## 每个包更新的内容： ### DOyulab.db包：用于取代DO.db。 包含如下数据： ```r > ls("package:DOyulab.db") [1] "DO" "DO_dbconn" "DO_dbfile" "DO_dbInfo" "DO_dbschema" "DOALIAS" "DOANCESTOR" "DOCHILDREN" "DOMAPCOUNTS" "DOOFFSPRING" "DOPARENTS" "DOSYNONYM" "DOTERM" ``` 我使用DO.db自带的Human.obo进行处理后生成DOyulab.db，将它与DO.db进行对比，DO id的数目以及DO id的祖先节点信息都完全相同，富集分析和语义相似性分析也完全相同，证明DOyulab.db的处理方式是正确的，除了更新数据外没有产生副作用。 与DO.db的区别：...
how can we add only a list of enriched terms in dotplot / cnetplot
Dear Guangchuang, Big fan of all the R suites your group develop! I have a question regarding the universal gene list used in the `enricher` function for the Over Representation...
### Prerequisites + [x] Have you read [Feedback](https://guangchuangyu.github.io/dose/#feedback) and follow the [guide](https://guangchuangyu.github.io/2016/07/how-to-bug-author/)? * [x] make sure your are using the latest release version * [x] read the [documents](https://guangchuangyu.github.io/dose/documentation/) * [x]...
### Prerequisites + [x] Have you read [Feedback](https://guangchuangyu.github.io/dose/#feedback) and follow the [guide](https://guangchuangyu.github.io/2016/07/how-to-bug-author/)? * [x] make sure your are using the latest release version * [x] read the [documents](https://guangchuangyu.github.io/dose/documentation/) * [x]...
Hi, This removes the need for a decreasing only sort if not using `DOSE`. In `is.sorted` decreasing was set to `TRUE` which also affected `fgsea`. Thank you, NelsonGon
把新的数据，https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkab1063/6424774， 和DO.db比一下，实在是多年没更新。 ``` > > x= readLines("HumanDO.obo") > x[which(x == "[Term]") +1] -> id > sub("id:\\s+", "", id) -> id > keys(DO.db::DOTERM) -> id2 > table(id %in% id2) FALSE TRUE...
Dear Clusterprofiler-Team, being quite new to R I am struggling with the following problem: I have prepared a comma-delimited Excel file (.csv) with gene expression data: first column Gene Symbol,...
I have been having trouble with two DOSE functions: gseNCG and enrichDGN. In both cases when I try to use either function on my list of sorted geneIDs and corresponding...
