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VisiumHD: Reading in raw_probe_bc_matrix.h5 #300

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julienmortier opened this issue Apr 8, 2025 · 0 comments
Open

VisiumHD: Reading in raw_probe_bc_matrix.h5 #300

julienmortier opened this issue Apr 8, 2025 · 0 comments

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@julienmortier
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spatialdata_io.visium_hd() now allows users to select between 'raw_feature_bc_matrix.h5' and 'filtered_feature_bc_matrix.h5', but in the output of Space Ranger, there is also the 'raw_probe_bc_matrix.h5' file, which allows the analysis of counts on a probe-level (instead of collapsing the counts of all probes into a single feature). While more niche, there are definitely situations where it would be very valuable if spatialdata_io.visium_hd() would support reading in this file (e.g. in cases of (partial) gene deletions) as well.

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