Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Advanced dea #37

Open
wants to merge 35 commits into
base: master
Choose a base branch
from
Open

Advanced dea #37

wants to merge 35 commits into from

Conversation

Alexandre-So
Copy link
Contributor

@Alexandre-So Alexandre-So commented Dec 16, 2021 •
edited
Loading

This include multiple factor differential expression analysis, as well as minor changes :

  • User can now select more than one condition for reference and perturbation
    • Add a function that create a balanced versus design giving a vector of conditions, and two vectors with the conditions to compare.
    • Modify the differential expression function to take this into account
    • The original function has been kept in the fct_dea.R file with the suffix "legacy". So it's still usable for comparison purpose.
  • Add a raw pvalue histogram
  • Add a tab showing the content of the edgeR fitted model. Note : the small description of this tab is not finished, there is a message saying "this text could be improve".
  • Change the color of the field separator to green in the import data page (not sure if it's better or not). Same for questions marks.
  • Remove the ugly red/blue borders of the Venn diagram

Alexandre-So and others added 30 commits October 12, 2021 12:12
@Alexandre-So
Modify DEA function to allow multiple input conds
464ba80 
The old function has been saved as "legacy".
@Alexandre-So
Allow multiple conditions DEA in shiny app
73a2515 
Users can now select multiple conditions, and can select how DEA genes
will be outputed. Also clearly write which conditions are selected.
@Alexandre-So
Add a step for fdr cutoff selection
dbc0e10
@Alexandre-So
Add missing comma in estimateDEG
ea3c49a
@Alexandre-So
Add multiple condition DEA support for clustering
974d813
@Alexandre-So
Remove useless print message
f70600c
@Alexandre-So
Test of pvalue histogram. Not very nice
fc44cd6
@Alexandre-So
Add a function for raw pvalue histogram plot
76b5696 
Add a function to display a raw pvalue histogram plot using ggplot2, and
integrate this function into DIANE interface.
@Alexandre-So
Improve multiple DEA fold change accuracy
bb48eb9 
When creating the versus design, values are no longer computed for
summing up to 1.
@Alexandre-So
Add a raw pvalue histogram plot
18a177d
@Alexandre-So
Small docs improvement
cc55b11
@Alexandre-So
Merge branch 'master' into advanced_DEA
e0597aa 
Some hotfix were added to master.
@Alexandre-So
Merge with master and remove conflicts
d16139b
@Alexandre-So
Multiple DEA cons are now handle by the heatmap
7924f3e 
I'm using a regex to extract condition name. This will work in the vast
majority of cases. But maybe there is a better way to proceed.
@Alexandre-So
Change color of question mark
b08c33e
@Alexandre-So
Remove systematic orientation parameter
1ced255
@Alexandre-So
Display multiple DE equation
202cbe7
@Alexandre-So
Display an equation of multiple DEA
2a6412e
@Alexandre-So
Fold change is use for raw pvalue hist
7c934bd
@Alexandre-So
Add a tab to display r$fit. Also small minor fix
ffd5f5c 
pvalue histogram is now also based on lfc. Add a small text under this
plot. Add a "versus" in the downloaded file name.
@Alexandre-So
pvalue histogram take a lfc cutoff arg
8733935
@Alexandre-So
fix weird Venn diagram border color
e291131
@Alexandre-So
Change radioButtons to awesomeRadio
97a8f02 
This allow to set the color of the buttons to green (success).
@Alexandre-So
Minor corrections
1b41d59 
- Remove a warning from pvalue plot
- Display perturbation / refrence instead of reference / perturbation in
  the help tab for multiple condition DEA
- Add some help text for the fit tab and the pvalue histogram
@Alexandre-So
Merge upstream/master into advanced_DEA
0b1350f 
Merge remote-tracking branch 'upstream/master' into advanced_DEA
@Alexandre-So
Remove useless comma
beb16b3
@Alexandre-So
Small minor text changes
0e3e7bf
@Alexandre-So
Change regex for DEA names/conditions in clustering part
e6929b2
@Alexandre-So
Add a sentence about multi-factor DGE
8f53f50
@Alexandre-So
Update condition extraction regex
11f9995
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
1 participant
@Alexandre-So