Build SpatialExperiment object

lmweber / locus-c

Code to reproduce analyses in our paper on the landscape of gene expression in the human locus coeruleus (LC)

MIT License

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Closed lmweber closed 3 years ago

lmweber commented 3 years ago

Build SpatialExperiment object containing data from all samples (all 3 rounds) in a single object:

Notes:

include metadata column for round IDs
add VistoSeg outputs from count_spots.csv files
re-order rows (barcodes) from count_spots.csv files to match row ordering in SPE object
save final SPE object

lmweber commented 3 years ago

lmweber commented 3 years ago

Move script into subdirectory

lmweber commented 3 years ago

Output SPE object is saved here:

/dcs04/lieber/lcolladotor/pilotLC_LIBD001/locus-c/processed_data/SPE/LC_rounds1to3_SPE.rds

lmweber commented 3 years ago

Moved into subdirectory in commit 9eced1b693315c26e2dd79f73189d961fddf6d77

Script is now here

lmweber commented 3 years ago

To do:

update column names in spatialCoords to x and y
remove outs/ in read10xVisium() call if we update this in SpatialExperiment package