UMAPs without mitochondria #1
Closed
Conversation
This file contains 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
… generate associated files for the new 'rsem_stranded_no-mito_log' filename_lead value
…erated stranded rsem without mito umap
|
Since this is in my fork I can't quite request reviewers so I will tag @jashapiro and @jaclyn-taroni. |
|
After further conversation we're going to wait on this to merge into the main repo, so I'll close this. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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Outdated suggestions cannot be applied.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.
initiate-tumor-purity-modulebranch which has an open PR into OpenPBTA here: AlexsLemonade#1622 (stacked b/c this consumes results from that PR).This PR explores dimension reduction without including mitochondrial genes, as inspired by this issue: AlexsLemonade#1601
There are two main changes here:
transcriptomic-dimension-reductionmodule to include an option to remove mitochondrial genes. I added this run for stranded RSEM with log2 on in order to generate data for this exploration.transcriptomic-dimension-reductionto explore the mitochondrial expression, first via just looking at FPKMs of mito genes for relevant diagnoses and then via UMAPs made with and without mitochondrial genes. I don't see anything too different here, but welcome thoughts on interpretation. Here's that notebook:05-seq-center-mitochondrial-genes.nb.html.zip