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Xenium

note

Spatial transcriptomics platform from 10x Genomics that provides subcellular resolution.

https://www.10xgenomics.com/platforms/xenium

Xenium is a spatial transcriptomics platform from 10x Genomics that provides subcellular resolution.

NOTE: parsing huge files is not an intended MultiQC usage. By default, MultiQC will ignore the *.parquet files as they are gigabyte-sized. To enable parsing those, make sure to have this line in your config:

log_filesize_limit: 5000000000 # 5GB

File search patterns

xenium/cell_feature_matrix:
fn: cell_feature_matrix.h5
xenium/cells:
fn: cells.parquet
xenium/experiment:
fn: experiment.xenium
num_lines: 50
xenium/metrics:
contents: num_cells_detected
fn: metrics_summary.csv
num_lines: 5
xenium/transcripts:
fn: transcripts.parquet