Three figures from Braun data analysis#29
Merged
Conversation
ksea_heatmap.Rmd - Uses KSEApp to estimate the Kinase activity in 5 contrasts, then plots a heatmap of the results. beataml_subtypes_pca.Rmd - Plots the pca of the common features between the beataml210 cohort and the Braun dataset, coloring by subtype. deconvolution_pca.Rmd - Shows the pca of the estimated cell composition of the Braun + BeatAML data. Also plots individual boxplots of the cell type values for the Braun data.
…amlMultidrugResistance into origin/add_scripts
CamiloPosso
changed the title
Small path error when sourcing, added source calls to the Rmds to fix this.
Member
|
Can you create a readme that summarizes the analysis, describes where the data reside, and cites the preprint? I made some minor changes to install less common packages as well. Synapse link should point here: https://www.synapse.org/Synapse:syn64021143 |
Added a comment or two Also added install for less common packages.
sgosline
approved these changes
Mar 13, 2026
Member
sgosline
left a comment
sgosline
left a comment
There was a problem hiding this comment.
In general the code is in good shape (though could use a bit more comments). The markdowns require a lot more description: what are you trying to show, and why? generally there is a scientific question underlying the analysis that will be answered.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Adding three figure markdowns