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Development #37

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@rachadele rachadele commented Nov 7, 2025

Major changes:

  • add support for multiple levels of granularity, submitted as two separate CTA files (class_cell_type and subclass_cell_type)

@rachadele
remove deprecated references
09059af
@rachadele
change taxonomy
b375cb1
@rachadele
make cell type renaming hierarchical
6d25b04
@rachadele
remove comments
4b009b9
@rachadele
fit classifier to subclass values
50f82f3
@rachadele
classify cells at multiple levels of granularity and map ontology terms
f2c8969
@rachadele
update version
6fbe44c
@rachadele
update main script
3a85c0c
@rachadele
update default cutoff
d40ecbe
@rachadele
write levels fo granularity to separate files
7caa6ee
@rachadele
add comment
687a719
@rachadele
change default work to cosmos
af179fc
@rachadele
update default ref collections
5ba5225
@rachadele
update aggregation logic
0d11789
@rachadele
update hsap renaming
03de101
@rachadele
fix logic to use ref keys argument instead of hardcoded column names
4833d1b
@rachadele
update params to use development branch rename files
548fbad
@rachadele
update tests to use existing MEX
8c3184d
@rachadele
add ref keys param
a8f655f
@rachadele
use ref keys for qc report
7492e7a
@rachadele
try to fix cell type matrices
1ca8a63
@rachadele
restore
c44c021
@rachadele
fix error in taxonomy mapping and add QC reporting for cell type key …
e20f95e 
…argument
@rachadele
change logic to account for multiple cell type files when processing …
bb26068 
…samples individually
@rachadele
add tags
a9c68e8
@rachadele
fix loadCTA
deca829
@rachadele
add tags
55382c5
@rachadele
fix CTA loading
1024e39
@rachadele
fix qc plotting
63bad02
@rachadele
fix cell type column rename
00ad445
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@rachadele