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API
Reading and writing data:
io
scmorph.io.read
scmorph.io.read_cellprofiler_csv
scmorph.io.read_cellprofiler_batches
scmorph.io.read_sql
scmorph.io.make_AnnData
scmorph.io.split_feature_names
Quality Control:
qc
scmorph.qc.filter_outliers
scmorph.qc.read_image_qc
scmorph.qc.qc_images
Preprocessing:
pp
scmorph.pp.drop_na
scmorph.pp.scale
scmorph.pp.scale_by_batch
scmorph.pp.remove_batch_effects
scmorph.pp.select_features
scmorph.pp.corr
scmorph.pp.kruskal_test
scmorph.pp.kruskal_filter
scmorph.pp.aggregate
scmorph.pp.aggregate_ttest
scmorph.pp.tstat_distance
scmorph.pp.aggregate_pc
scmorph.pp.aggregate_mahalanobis
scmorph.pp.pca
scmorph.pp.neighbors
scmorph.pp.umap
Visualization:
pl
scmorph.pl.pca
scmorph.pl.umap
scmorph.pl.cumulative_density
scmorph.pl.ridge_plot
Analysis tools:
tl
scmorph.tl.get_ks
scmorph.tl.slingshot
scmorph.tl.test_common_trajectory
scmorph.tl.test_differential_differentiation
scmorph.tl.test_differential_progression
Datasets:
datasets
scmorph.datasets.rohban2017
scmorph.datasets.rohban2017_minimal
scmorph.datasets.rohban2017_imageQC
scmorph.datasets.rohban2017_minimal_csv
Tutorials
Basic workflows
Batch effects
Feature selection
Hit calling
Changelog
Contributing guide
References
.md
.pdf
Basic workflows
Basic workflows
#
Batch effects
Feature selection
Hit calling
