ReactomePA

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Hello, I have tried looking through previous issue reports and have not found this issue addressed, yet. I am using enrichPathway and gsePathway in a custom loop to analyze a...

pschumann4

I run the function "enrichPathway", the organism can only be chosen as one of "human", "rat", "mouse", "celegans", "yeast", "zebrafish", "fly". So, what can i do if I want to...

LongYuan0529

"No gene can be mapped" when running enrichPathway

4

Hi, Thanks for establishing the R-based Reactome tool. I want to do a pathway analysis based on a list of mouse genes, but when I tried the function `enrichPathway`, an...

RuiyangLiu94

Hey, first: thank you for the package along with the data comprehensive book/vignette, it's great! I was digging a bit deeper in the original Reactome analysis provided by the web-tool...

L3ft2di3

### Prerequisites + [X] Have you read [Feedback](https://guangchuangyu.github.io/reactomepa/#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/reactomepa/documentation/) * [X]...

Jay-Leung

### Prerequisites + [x] Have you read [Feedback](https://guangchuangyu.github.io/reactomepa/#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/reactomepa/documentation/) * [x]...

Nelson-Gon

Specify minimal package versions in the Description file

2

### Prerequisites + [x] Have you read [Feedback](https://guangchuangyu.github.io/reactomepa/#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/reactomepa/documentation/) * [x]...

Nelson-Gon

Hello, I have 482 ensembl genes (411 tranformed into entrz using bitr) to perform Reactome pathway gene erichment analysis. I used the ReactomePA and kobas-i at the same time, with...

Freya-Cui-2020

No gene can be mapped with gsePathway

2

Hello, I am trying to run reactomePA for my DE genes. I manage to run enrichPathway successfully (`yy = enrichPathway(genes$entrezgene_id, pvalueCutoff=0.05)`), but when I do the following: ``` sorted_genes =...

alexandrafleming

Hello, I was wondering if it's possible to apply the package on WES VCF or MAF files? Kind regards Ivana

IvanaOsredek