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  1. IGB
  2. IGBF-4315

K means clustering strategy on pol data

        Details

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

          Description

          GOAL: To attempt to implement one of the various K-mean clustering strategies on Kelsey's Pollinated dataset.

          The reason: Her committee asked. This is to mostly silence them. Or maybe we will get some really cool insight!

          The input will be the deseq2 normalized data (not DSeseq results). No idea what tools we mgiht try yet. This ticket is to come up with a plan of attack. New tickets needed for actual implementation.

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              robofjoy Robert Reid created issue -
              robofjoy Robert Reid made changes -
              Field Original Value New Value
              Epic Link IGBF-2993 [ 21429 ]
              robofjoy Robert Reid made changes -
              Assignee Ann Loraine [ aloraine ] Robert Reid [ robertreid ]
              robofjoy Robert Reid made changes -
              Status To-Do [ 10305 ] In Progress [ 3 ]
              ann.loraine Ann Loraine made changes -
              Sprint Fall 2 [ 225 ] Fall 2, Fall 3 [ 225, 226 ]
              ann.loraine Ann Loraine made changes -
              Rank Ranked higher
              robofjoy Robert Reid made changes -
              Status In Progress [ 3 ] To-Do [ 10305 ]
              bbendick Brandon Bendickson made changes -
              Status To-Do [ 10305 ] In Progress [ 3 ]
              bbendick Brandon Bendickson made changes -
              Assignee Robert Reid [ robertreid ] Brandon Bendickson [ bbendick ]
              ann.loraine Ann Loraine made changes -
              Sprint Fall 2, Fall 3 [ 225, 226 ] Fall 2, Fall 3, Fall 4 [ 225, 226, 227 ]
              ann.loraine Ann Loraine made changes -
              Rank Ranked higher
              bbendick Brandon Bendickson made changes -
              Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
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              bbendick Brandon Bendickson added a comment -

              Several literature sources tell us that K-means is not effective for timecourse/multisample rna seq data, but to use model based clustering instead. Shifting to a tool called mClust in R

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              bbendick Brandon Bendickson added a comment - Several literature sources tell us that K-means is not effective for timecourse/multisample rna seq data, but to use model based clustering instead. Shifting to a tool called mClust in R
              bbendick Brandon Bendickson made changes -
              Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
              bbendick Brandon Bendickson made changes -
              Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
              bbendick Brandon Bendickson made changes -
              Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
              bbendick Brandon Bendickson made changes -
              Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
              bbendick Brandon Bendickson made changes -
              Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
              bbendick Brandon Bendickson made changes -
              Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
              bbendick Brandon Bendickson made changes -
              Resolution Done [ 10000 ]
              Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                People

                • Assignee:
                  bbendick Brandon Bendickson
                  Reporter:
                  robofjoy Robert Reid
                • Votes:
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                  Dates

                  • Created:
                    Updated:
                    Resolved: