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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.qc_images_by_dissimilarity
scmorph.qc.count_cells_per_group
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.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
Image QC
Batch effects
Feature selection
Hit calling
Explainer notebooks
Comparison of batch effect correction techniques
Comparison of correlation coefficients
Changelog
Contributing guide
Community
References
.md
.pdf
Basic workflows
Basic workflows
#
Image QC
Batch effects
Feature selection
Hit calling
