[IGBF-4137] Checking the feasibility of Cluster Profiler - JIRA UNCC

Details

Type: Task
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: None
Labels:
None

Story Points:
1
Epic Link:
Support NSF pollen grant
Sprint:
Spring 3

Description

GOAL: Compared to CDHIT, would Cluster Profiler in R be a better or worse option for grouping our de novo gene sets.

https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html

Read through, summarize this tools function? Would it be of value to our project?

Attachments

Activity

Ascending order - Click to sort in descending order

Robert Reid created issue - 12/Mar/25 10:23 AM

Robert Reid made changes - 12/Mar/25 10:23 AM

Field	Original Value	New Value
Epic Link		IGBF-2993 [ 21429 ]

Brandon Bendickson made changes - 12/Mar/25 12:53 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Hide

Permalink

Brandon Bendickson added a comment - 14/Mar/25 10:59 AM

Cluster Profiler does not perform any clustering or grouping, but rather its a series of R tools that perform functional enrichment.
"It provides a tidy interface to access, manipulate, and visualize enrichment results to help users achieve efficient data interpretation."

One tool of interest could be "compareCluster" this tool compares already existing clusters (our CD-HIT results) and computes functional profiles for each one.

However in terms of grouping our de novo gene sets, CD-HIT is still a better option, but ClusterProfiler may come in handy for later analyses.

Show

Brandon Bendickson added a comment - 14/Mar/25 10:59 AM Cluster Profiler does not perform any clustering or grouping, but rather its a series of R tools that perform functional enrichment. "It provides a tidy interface to access, manipulate, and visualize enrichment results to help users achieve efficient data interpretation." One tool of interest could be "compareCluster" this tool compares already existing clusters (our CD-HIT results) and computes functional profiles for each one. However in terms of grouping our de novo gene sets, CD-HIT is still a better option, but ClusterProfiler may come in handy for later analyses.