[IGBF-4145] Tweaking Deseq2 script in incorporate ComplexUpsetR - 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:
3
Epic Link:
Support NSF pollen grant
Sprint:
Spring 4

Description

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

2 strategies:

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

Attachments

Activity

Ascending order - Click to sort in descending order

Robert Reid created issue - 19/Mar/25 8:42 AM

Robert Reid made changes - 19/Mar/25 8:42 AM

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

Hide

Permalink

Robert Reid added a comment - 19/Mar/25 8:43 AM

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

Show

Robert Reid added a comment - 19/Mar/25 8:43 AM Step 1: Rob needs to share the original script, the metafile and the FeatureCount counts table.

Brandon Bendickson made changes - 19/Mar/25 8:56 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Hide

Permalink

Robert Reid added a comment - 19/Mar/25 9:00 AM

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

Show

Robert Reid added a comment - 19/Mar/25 9:00 AM First step is get the pieces and test that the Deseq2 is working correctly up to line 390, the section where UpsetR begins.

Hide

Permalink

Brandon Bendickson added a comment - 24/Mar/25 11:38 AM

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

Show

Brandon Bendickson added a comment - 24/Mar/25 11:38 AM Got all pieces and code to work until line 390, writing new python script to generate "input4complex.tsv"

Robert Reid made changes - 24/Mar/25 2:11 PM

Description	GOAL: To take an existing Deseq2 script and add the ability to run ComplexUpsetR within the script. 2 strategies: # Run Brandon's python script to prep the table and then run upsetR. # Use Tidyverse features to manipulate the Deseq results to prep for UpsetR	GOAL: To take an existing Deseq2 script and add the ability to run ComplexUpsetR within the script. 2 strategies: # Run Brandon's python script to prep the table and then run upsetR. # Use Tidyverse features to manipulate the Deseq results to prep for UpsetR
Story Points	2	3

Hide

Permalink

Brandon Bendickson added a comment - 25/Mar/25 3:32 PM

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

Show

Brandon Bendickson added a comment - 25/Mar/25 3:32 PM Fixed script to include upsetR at the end. Also wrote accompanying python script for generating the input and integrated it into overall script.