Adding ReadAlevin function [WIP] #896
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
If the data used for the regression contains NA values, this will lead to errors downstream. For example, if one row contains an NA value, it will be removed and create a size mismatch when a data.frame is later constructed using the residuals of all rows, or if a linear model is used, it will create a problem when the QR values are reused.
Warn on NA data being used for regression
…n of genes.tsv to use as gene names
|
Hi Avi, I know this is a work in progress, but could you make sure you're building off of the |
|
Sounds good @mojaveazure , thanks for the heads up ! |
|
Hi @mojaveazure , I have the relevant changes ready in the forked seurat repo in an updated |
|
Hi Avi, whichever's easiest for you. A new PR might be cleaner, but it's up to you. |
|
Thanks @mojaveazure , I'll make a new one then and close this one. |
dcollins15
added a commit
that referenced
this pull request
Feb 15, 2024
Fixes for SCTransform using `vars.to.regress`
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Outdated suggestions cannot be applied.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.
Hi Seurat team,
First of all thanks for the awesome tool, it has helped us and our user base a lot in analyzing the scRNA-seq data.
We have recently developed a dscRNA-seq quantification pipeline with name
Alevin(preprint here), and we frequently encounter feature requests from our user base regarding the preprocessing of the reads for subsampling/batch correction like COMBINE-lab/salmon#305. We generally recommend users to go through this tutorial to parse the Alevin output and perform bias correction through Seurat package downstream of Alevin. In lieu of that to simplify the clustering pipeline by one more step we'd love to make the following pull request to parse the Alevin output and would really appreciate, if possible, to optimize the committed parsing function and merge to master in your next release.Alevin dumps both
csvand a more efficient binary format. We are working on writing a parser for the binary format and would update this pull request soon. As a noob inRI'd appreciate if you see something horribly wrong in the committed parsing code and would appreciate your feedback.