clusterProfiler | universal enrichment tool for interpreting omics data | Genomics library

by YuLab-SMU R Version: Current License: No License

X-Ray Key Features Code Snippets Community Discussions(5)Vulnerabilities Install Support

kandi X-RAY | clusterProfiler Summary

clusterProfiler is a R library typically used in Artificial Intelligence, Genomics applications. clusterProfiler has no bugs, it has no vulnerabilities and it has medium support. You can download it from GitHub.

This package implements methods to analyze and visualize functional profiles of genomic coordinates (supported by ChIPseeker), gene and gene clusters. For details, please visit

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clusterProfiler has a medium active ecosystem.

It has 779 star(s) with 237 fork(s). There are 48 watchers for this library.

It had no major release in the last 6 months.

There are 231 open issues and 283 have been closed. On average issues are closed in 36 days. There are 2 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of clusterProfiler is current.

Quality

clusterProfiler has 0 bugs and 0 code smells.

Security

clusterProfiler has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

clusterProfiler code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

clusterProfiler does not have a standard license declared.

Check the repository for any license declaration and review the terms closely.

Without a license, all rights are reserved, and you cannot use the library in your applications.

Reuse

clusterProfiler releases are not available. You will need to build from source code and install.

It has 275 lines of code, 0 functions and 2 files.

It has low code complexity. Code complexity directly impacts maintainability of the code.

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clusterProfiler Key Features

No Key Features are available at this moment for clusterProfiler.

clusterProfiler Examples and Code Snippets

No Code Snippets are available at this moment for clusterProfiler.

Community Discussions

Trending Discussions on clusterProfiler

How to convert Entrez ids in a large list into gene symbols and replace entrez ids in list in R?

How to add to a cnetplot using ggplot functions?

Cannot specify input dataset in shiny dashboard

Mapping nothing when doing Enrichment Analysis of the TAIR using enrichGO in R

CentOS7 using R to install clusterProfiler get error about openssl

QUESTION

How to convert Entrez ids in a large list into gene symbols and replace entrez ids in list in R?

Asked 2022-Feb-03 at 17:57

I have a large list data with 300 names. For eg:

...

ANSWER

Answered 2022-Feb-03 at 17:57

We may loop over the list and apply the bitr

Source https://stackoverflow.com/questions/70975616

QUESTION

How to add to a cnetplot using ggplot functions?

Asked 2021-Oct-01 at 23:13

I have a dataset in R that is a class of 'Formal class enrichResult'. I plot the genes in this dataset using cnetplot() from the package DOSE - which is meant to be based on ggplot graphics. This plots a network of genes in interacting pathways:

I code for this with:

...

ANSWER

Answered 2021-Oct-01 at 23:13

I used the clusterProfiler example to make the code reproducible (https://yulab-smu.top/biomedical-knowledge-mining-book/universal-api.html)
I used the categories.tsv file from (https://www.dgidb.org/downloads)

Source https://stackoverflow.com/questions/69121983

QUESTION

Cannot specify input dataset in shiny dashboard

Asked 2021-Aug-01 at 13:05

I am trying to make a shiny dashboard. I have two datasets, and based upon the selection of the datasets figures will be generate in the tab panels. However, by default only the last dataset that has been loaded/read is selected and I cannot select the first dataset. Even though I have made it default selection.

Below is my code.

...

ANSWER

Answered 2021-Aug-01 at 13:05

Assuming you have access to both datasets, you plot them both and display the selection. Try this

Source https://stackoverflow.com/questions/68606165

QUESTION

Mapping nothing when doing Enrichment Analysis of the TAIR using enrichGO in R

Asked 2021-May-17 at 14:56

I tried to do Enrichment Analysis of Arabidopsis thaliana by using enrichGO with R. But the result is empty. What caused this result?

...

ANSWER

Answered 2021-May-17 at 14:56

setting/including the arguments pAdjustMethod = "none", pvalueCutoff = 1, and qvalueCutoff = 1.

Source https://stackoverflow.com/questions/67571127

QUESTION

CentOS7 using R to install clusterProfiler get error about openssl

Asked 2021-May-16 at 14:56

I've been having an unresolved error when I installed clusterProfiler using R on CentOS7. I have checked the information and some of them say it is the reason for installing the openssl version at the same time, but I have not found a specific solution.

...

ANSWER

Answered 2021-May-16 at 14:56

do this operation can solve the problem:

yum install openssl-devel

yum info openssl-devel

pkg-config --modversion openssl

Source https://stackoverflow.com/questions/67557208

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install clusterProfiler

You can download it from GitHub.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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