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refactor: use dance transformations in clustering example scripts #189

Merged
merged 15 commits into from
Feb 15, 2023
Merged

refactor: use dance transformations in clustering example scripts #189

merged 15 commits into from
Feb 15, 2023

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RemyLau
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@RemyLau RemyLau commented Feb 15, 2023 •
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Note: still need to update graphsc, which might require a bit engineering.

@RemyLau RemyLau marked this pull request as ready for review February 15, 2023 21:37
RemyLau added 15 commits February 15, 2023 16:39
@RemyLau
add X and raw_X options to channel_type and schedule deprecation for …
54e927b 
…channel=None
@RemyLau
update docstring and add warning coment
9dc9b6f
@RemyLau
extract feature from the dance data object for sctag
23197ec
@RemyLau
use dance transforms in sctag
4908f99
@RemyLau
refactor _get_feature to reduce cyc complexity
e2082e4
@RemyLau
implement SaveRaw transformation
1ae1494
@RemyLau
pass n_counts instead of scale_factor
afe8eb6
@RemyLau
replce all transformations with dance transform
d62e265
@RemyLau
remove unused imports
a81d188
@RemyLau
pass n_counts to scdcc as input instead of scale/size factor
a8da5b7
@RemyLau
refactor scdcc example script to use dance transform
b1cbc94
@RemyLau
update scdsc example script to use dance transformations
b98b365 
- Pass n_counts instaed of size factor
- Use sc.pp.neighbors to camppute the knn graph, the correlation metric is not the same as
  that implemented in the original repo, which seems to be incorrect (DHUDBlab/scDSC#3)
@RemyLau
deprecate PretrainDataset and TrainingDataset from scDSC
225a9f6
@RemyLau
remove deprecated transforms
2f191bf
@RemyLau
update scdeepcluster example script to use dance transformations
2b595dd
@RemyLau RemyLau merged commit 9a21eb2 into main Feb 15, 2023
@RemyLau RemyLau deleted the update-clustering branch February 15, 2023 21:55
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@RemyLau