SRR28679756_raw_matrix.h5ad converted to 10x Matrix Market format#2046
Merged
Conversation
For testing cellbender/removebackground with 10x Matrix Market input
13 tasks
There was a problem hiding this comment.
Pull request overview
Note
Copilot was unable to run its full agentic suite in this review.
Adds documentation for a converted scRNA-seq gene expression matrix (SRR28679756) in 10x Matrix Market format to support testing cellbender/removebackground with 10x-style inputs.
Changes:
- Add a README describing the 10x Matrix Market output files (matrix/barcodes/features).
- Document the mapping/limitation that
features.tsv.gzlacks gene IDs and repeats gene names.
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
| Conversion of modules/data/genomics/homo_sapiens/scrnaseq/h5ad/SRR28679756_raw_matrix.h5ad into 10X-style Matrix Market format, i.e. 3 files: | ||
| - matrix.mtx.gz: Matrix Market sparse matrix | ||
| - barcodes.tsv.gz: 1 column, no header, with cell barcodes that are the column names of matrix.mtx.gz | ||
| - features.tsv.gz: 3 columns, no header, with gene_name, gene_name, "Gene Expression" |
nictru
approved these changes
Jun 25, 2026
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
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
For testing cellbender/removebackground with 10x Matrix Market input