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  1. IGB
  2. IGBF-4137

Checking the feasibility of Cluster Profiler

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

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              bbendick Brandon Bendickson added a comment -

              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.

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              bbendick Brandon Bendickson added a comment - 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.

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                • Assignee:
                  bbendick Brandon Bendickson
                  Reporter:
                  robofjoy Robert Reid
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