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  1. IGB
  2. IGBF-4145

Tweaking Deseq2 script in incorporate ComplexUpsetR

        Details

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

          GOAL: To take an existing Deseq2 script and add the ability to run ComplexUpsetR within the script.

          2 strategies:

          1. Run Brandon's python script to prep the table and then run upsetR.
          2. Use Tidyverse features to manipulate the Deseq results to prep for UpsetR

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              bbendick Brandon Bendickson added a comment -

              Fixed script to include upsetR at the end. Also wrote accompanying python script for generating the input and integrated it into overall script.

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              bbendick Brandon Bendickson added a comment - Fixed script to include upsetR at the end. Also wrote accompanying python script for generating the input and integrated it into overall script.
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              bbendick Brandon Bendickson added a comment -

              Got all pieces and code to work until line 390, writing new python script to generate "input4complex.tsv"

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              bbendick Brandon Bendickson added a comment - Got all pieces and code to work until line 390, writing new python script to generate "input4complex.tsv"
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              robofjoy Robert Reid added a comment -

              First step is get the pieces and test that the Deseq2 is working correctly up to line 390, the section where UpsetR begins.

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              robofjoy Robert Reid added a comment - First step is get the pieces and test that the Deseq2 is working correctly up to line 390, the section where UpsetR begins.
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              robofjoy Robert Reid added a comment -

              Step 1: Rob needs to share the original script, the metafile and the FeatureCount counts table.

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              robofjoy Robert Reid added a comment - Step 1: Rob needs to share the original script, the metafile and the FeatureCount counts table.

                People

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

                  • Created:
                    Updated:
                    Resolved: