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

Revision #34

Merged
merged 59 commits into from
Jun 18, 2024
Merged

Revision #34

merged 59 commits into from
Jun 18, 2024

Conversation

miltondp
Copy link
Member

@miltondp miltondp commented Jan 3, 2024

No description provided.

miltondp and others added 30 commits September 1, 2023 11:09
@miltondp
references: fix article's year
fe00ada
@miltondp
update time test plot
0f4314e
@miltondp
update time test plot
53e5852
@miltondp
revise/split long paragraphs
8fcbe9a
@miltondp
introduction: remove repeated word
b131743
@miltondp
abstract: add a sentence with more details about CCC
8b991f9
@miltondp
change title
6aecb45
@miltondp
results/overview: change subsection title
eacf766
@miltondp
results/overview: explain how CCC works with categorical values
af81e51
@miltondp
references: use PhenoPLIER new DOI
6cf5e86
@miltondp
Merge branch 'main' into revision
6057b4e
@miltondp
add figures to response to Reviewer 2 about UTY and KDM6A
3158cb5
@miltondp
add analysis of CCC with a cluster data structure
295064d
@miltondp
supplementary material: use S1, S2, etc for supplementary figures and…
58a67e1 
… tables.
@miltondp
methods: add link to CCC algorithm
438e21a
@miltondp
add Vinh paper
2dbe717
@miltondp
figure 1: update to include p-values in numerical examples
3071160
@miltondp
add work-in-progress changes to Methods
6b57136
@miltondp
add work-in-progress changes to Results
ad45e6a
@miltondp
fix references to subfigures
8c0811a
@miltondp
results: minor change
ab6a03b
@miltondp
freeze references
8ed9665
@miltondp
update figure 3b with new gene pairs
e14afea
@miltondp
update Table S1 using new gene pairs
473e571
@miltondp
update figure 5c using FDR < 0.05, although no noticeable changes
fdf7ad6
@miltondp
figure 4 and S3: update kdm6a vs uty in GTEx tissues and add kdm6a vs…
33ef7aa 
… ddx3y
@miltondp
figure 1: extend it with categorical variables
4229352
@miltondp
figure S2 (time test): resize huge white background
6fba39c
@miltondp
results/comp: update comparison with others and nonlinear gene pairs …
f82c6fb 
…descriptions
@miltondp
results/giant: revise text and update figure 5
9154ea8
miltondp added 13 commits January 5, 2024 15:33
@miltondp
discussion: mention methods to limit number of permutations
e1c2212
@miltondp
discussion: minor improvement
481d40e
@miltondp
methods: add more details about the CCC and update algorithm
21ea7e7
@miltondp
supplementary material: put figures and tables in their specific sect…
6eea17c 
…ions
@miltondp
supplementary material: minor update to table title
ec10684
@miltondp
supplementary material: add figure with analyses on constant baseline…
422cea0 
… property
@miltondp
methods: update section about k_max
01a51ab
@miltondp
supplementary note 1: first draft of section comparing CCC and MIC co…
14c49a5 
…nceptually and statistically
@miltondp
supplementary note 1: update CCC vs MIC section
734a4fc
@miltondp
methods: minor update in the definition of partitions with categorica…
3f10aab 
…l data
@miltondp
add code and data availability section
1d9d709
@miltondp
methods: fix page break
f65b43f
@miltondp
supplementary material: improvements in section comparing CCC and MIC
b0585cd
@miltondp miltondp requested a review from cgreene January 9, 2024 00:03
@miltondp miltondp marked this pull request as ready for review January 9, 2024 00:04
miltondp and others added 13 commits May 16, 2024 22:22
@miltondp
CCC algorithm: minor improvement
912c42a
@miltondp
discussion: add note about potential confounders from reviewer's comment
216597e
@miltondp
methods: minor fix
c360dd5
@miltondp
supplementary material: move paragraph with conceptual difference bet…
7bca5e7 
…ween CCC and MIC to the top
@miltondp
supplementary material: fixes and minor improvements
536bae6
@miltondp @dmilone
figure 1: apply Diego's suggestions to caption
d0721af 
Co-authored-by: Diego Milone <[email protected]>
@miltondp @dmilone
figure 1: adjust strength of categorical dataset
a4eaf23 
Co-authored-by: Diego Milone <[email protected]>
@miltondp @dmilone
results/intro: incorporate Diego's suggestions
0d8eab6 
Co-authored-by: Diego Milone <[email protected]>
@miltondp
figure 1: update text
ba5dbee
@miltondp @dmilone
results: add Diego's suggestions
cc06ba9 
Co-authored-by: Diego Milone <[email protected]>
@miltondp @dmilone
methods: add Diego's suggestions
e085563 
Co-authored-by: Diego Milone <[email protected]>
@miltondp @dmilone
supplementary material: add Diego's suggestions
6472dc3 
Co-authored-by: Diego Milone <[email protected]>
@miltondp
methods/data: add GTEx v8 URL
28c2721
@miltondp miltondp merged commit 3c71849 into main Jun 18, 2024
1 check passed
@miltondp miltondp deleted the revision branch June 18, 2024 19:50
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@cgreene cgreene Awaiting requested review from cgreene

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
@miltondp