Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:4
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Sprint:Fall 4 2023 Oct 16, Fall 5
Description
Use Ivory's app.R from inducible-ant-rna-seq repo and adapt it to our own results.
Files to use:
- CvT-DESeq2-[assembly].txt
- muday-144-[assembly]_counts-salmon_scaled.txt
- muday-144_sample_sheet.xlsx
Attachments
Issue Links
- relates to
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-3446 [ 22548 ] |
Update since 1st demo:
- App now includes SL4 and SL5 genes
- Includes all experiments in the data frame for user to see
- Removed scientific notation
- Added note about NA
- Having some issues with getting all the data to show up for each experiment with the chosen gene
- Currently working on main plots
Ann Barplot Resource: https://bitbucket.org/aloraine/flavonoid-rnaseq/branch/IGBF-3449-1
| Description |
Use Ivory's app.R from inducible-ant-rna-seq repo and adapt it to our own results.
|
Use Ivory's app.R from inducible-ant-rna-seq repo and adapt it to our own results.
Files to use: * CvT-DESeq2-[assembly].txt * muday-144-[assembly]_counts-salmon_scaled.txt * muday-144_sample_sheet.xlsx |
| Sprint | Fall 4 2023 Oct 16 [ 180 ] | Fall 4 2023 Oct 16, Fall 5 [ 180, 181 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
Ann recommends: Put the work on a branch with a name that indicates this is a work in progress (e.g., IGBF-3480-wip, or whatever makes sense to the developer) and then add this branch to the team repository by a submitting a PR, where the PR is not merging but simply pushing the new branch to the team repo.
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Please make a NEW branch and push the new branch to the team repository. The "target" branch should be the same branch name.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Comment |
[ *PR*: https://bitbucket.org/hotpollen/flavonoid-rnaseq/pull-requests/34
Note: This is to save my work on a branch and to ensure no work is lost. I will continue working on the app. ] |
| Summary | Adapt Ivory Shiny app to work with our Lab results | Investigate: Adapt Ivory Shiny app to work with our Lab results |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Molly Davis [ molly ] | Ann Loraine [ aloraine ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Ann Loraine [ aloraine ] | Molly Davis [ molly ] |
Update: I have made my own app.R and have been adding each step of Ivory code into the app over time. For example, I have successfully used our results file and was able to adapt the code to show the gene identifier and to check it. I also posted the correct gene name below the user input with an else statement that will give corrections if wrong. Right now I am working on the data.frame in the sidebar under the gene identifier so it works with our results file.