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:3
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Sprint:Fall 2 2023 Sep 17
Description
The time course data set includes genotypes are, VF36, F3H
For this task, create some code that tests the interaction between temperature and genotype.
Note: We will have results for every time point individually.
Goal: Find genes that respond differently to heat stress depending on genotype.
For example, is there a gene that increases expression in response to heat in the "are" genotype and decreases expression in response to heat in the "VF36" genotype?
Suggestions for how to do these things:
- Read section from DESeq2 manual description testing of interactions between variables: https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#interactions
- review design creation: https://youtu.be/X6p3E-QTcUc?t=646
- This was also helpful: https://hbctraining.github.io/DGE_workshop/lessons/04_DGE_DESeq2_analysis.html
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link |
|
| Link | This issue relates to IGBF-3437 [ IGBF-3437 ] |
| Link | This issue relates to IGBF-3438 [ IGBF-3438 ] |
| Link | This issue relates to IGBF-3439 [ IGBF-3439 ] |
| Link | This issue relates to IGBF-3440 [ IGBF-3440 ] |
| Summary | Create DESeq Genotype and Time Designs for Muday-144 | Design genotype by temperature linear model-based design using DESeq2 |
| Summary | Design genotype by temperature linear model-based design using DESeq2 | Design genotype by temperature testing using DESeq2 |
| Description |
*Create the designs for new DESeq analysis'*
* review design creation: https://youtu.be/X6p3E-QTcUc?t=646 * ensure the designs answer Muday Labs questions about genotype and time * make sure to use the same designs for DESeq and EdgeR * run the analysis for both statistical methods twice for just genotype and then just time Ex Design: genotype + temperature and time + temperature analysis |
The time course data set includes genotypes are, VF36, F3H
For this task, create some code that tests the interaction between temperature and genotype. Goal: Find genes that respond differently to heat stress depending on genotype. For example, is there a gene that increases expression in response to heat in the "are" genotype and decreases expression in response to heat in the "VF36" genotype? Suggestions for how to do these things: * review design creation: https://youtu.be/X6p3E-QTcUc?t=646 |
| Summary | Design genotype by temperature testing using DESeq2 | Compare temperature responsiveness between genotypes using DESeq2 |
| Assignee | Molly Davis [ molly ] |
| Description |
The time course data set includes genotypes are, VF36, F3H
For this task, create some code that tests the interaction between temperature and genotype. Goal: Find genes that respond differently to heat stress depending on genotype. For example, is there a gene that increases expression in response to heat in the "are" genotype and decreases expression in response to heat in the "VF36" genotype? Suggestions for how to do these things: * review design creation: https://youtu.be/X6p3E-QTcUc?t=646 |
The time course data set includes genotypes are, VF36, F3H
For this task, create some code that tests the interaction between temperature and genotype. Note: We will have results for every time point *individually*. Goal: Find genes that respond differently to heat stress depending on genotype. For example, is there a gene that increases expression in response to heat in the "are" genotype and decreases expression in response to heat in the "VF36" genotype? Suggestions for how to do these things: * review design creation: https://youtu.be/X6p3E-QTcUc?t=646 |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Description |
The time course data set includes genotypes are, VF36, F3H
For this task, create some code that tests the interaction between temperature and genotype. Note: We will have results for every time point *individually*. Goal: Find genes that respond differently to heat stress depending on genotype. For example, is there a gene that increases expression in response to heat in the "are" genotype and decreases expression in response to heat in the "VF36" genotype? Suggestions for how to do these things: * review design creation: https://youtu.be/X6p3E-QTcUc?t=646 |
The time course data set includes genotypes are, VF36, F3H
For this task, create some code that tests the interaction between temperature and genotype. Note: We will have results for every time point *individually*. Goal: Find genes that respond differently to heat stress depending on genotype. For example, is there a gene that increases expression in response to heat in the "are" genotype and decreases expression in response to heat in the "VF36" genotype? Suggestions for how to do these things: * review design creation: https://youtu.be/X6p3E-QTcUc?t=646 & https://hbctraining.github.io/DGE_workshop/lessons/04_DGE_DESeq2_analysis.html |
| Description |
The time course data set includes genotypes are, VF36, F3H
For this task, create some code that tests the interaction between temperature and genotype. Note: We will have results for every time point *individually*. Goal: Find genes that respond differently to heat stress depending on genotype. For example, is there a gene that increases expression in response to heat in the "are" genotype and decreases expression in response to heat in the "VF36" genotype? Suggestions for how to do these things: * review design creation: https://youtu.be/X6p3E-QTcUc?t=646 & https://hbctraining.github.io/DGE_workshop/lessons/04_DGE_DESeq2_analysis.html |
The time course data set includes genotypes are, VF36, F3H
For this task, create some code that tests the interaction between temperature and genotype. Note: We will have results for every time point *individually*. Goal: Find genes that respond differently to heat stress depending on genotype. For example, is there a gene that increases expression in response to heat in the "are" genotype and decreases expression in response to heat in the "VF36" genotype? Suggestions for how to do these things: * Read section from DESeq2 manual description testing of interactions between variables: https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#interactions * review design creation: https://youtu.be/X6p3E-QTcUc?t=646 * This was also helpful: https://hbctraining.github.io/DGE_workshop/lessons/04_DGE_DESeq2_analysis.html |
| Assignee | Molly Davis [ molly ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Ann Loraine [ aloraine ] | Molly Davis [ molly ] |
| Assignee | Molly Davis [ molly ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Molly Davis [ molly ] |