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Installation
Basic Usage
Command-line interface
Tutorials
Organizing data, experiments, and projects
Command line tutorials
Experiment configuration CSV
API
Informatics:
inform
Preprocessing:
pp
Tools:
tl
smftools.tools.calculate_knn
smftools.tools.calculate_leiden
smftools.tools.calculate_nmf
smftools.tools.calculate_pca
smftools.tools.calculate_umap
smftools.tools.cluster_adata_on_methylation
smftools.tools.general_tools
smftools.tools.partitioned_hmm
smftools.tools.partitioned_spatial
smftools.tools.position_stats
smftools.tools.read_stats
smftools.tools.rolling_nn_distance
smftools.tools.sequence_alignment
smftools.tools.spatial_autocorrelation
smftools.tools.subset_adata
smftools.tools.tensor_factorization
Analysis:
an
smftools.analysis.compute.autocorrelation
smftools.analysis.compute.pearson
smftools.analysis.compute.hmm_features
smftools.analysis.compute.ep_classification
smftools.analysis.compute.ls_periodicity
smftools.analysis.compute.dimensionality_reduction
smftools.analysis.compute.metrics_store
smftools.analysis.compute.ml_cnn
smftools.analysis.compute.ml_metrics
smftools.analysis.compute.ml_splits
smftools.analysis.compute.read_cache
smftools.analysis.plot.heatmaps
smftools.analysis.plot.histograms
smftools.analysis.plot.autocorr
smftools.analysis.plot.embeddings
smftools.analysis.plot.locus
smftools.analysis.plot.ml
smftools.analysis.filters.obs_filters
smftools.analysis.filters.position_filters
smftools.analysis.config.hmm_histogram
Plotting:
pl
smftools.plotting.autocorrelation_plotting
smftools.plotting.chimeric_plotting
smftools.plotting.classifiers
smftools.plotting.general_plotting
smftools.plotting.hmm_plotting
smftools.plotting.latent_plotting
smftools.plotting.plotting_utils
smftools.plotting.pod5_plotting
smftools.plotting.position_stats
smftools.plotting.preprocess_plotting
smftools.plotting.qc_plotting
smftools.plotting.spatial_plotting
smftools.plotting.umi_plotting
smftools.plotting.variant_plotting
Datasets:
smftools.datasets.datasets
AnnData schema registry
Release notes
Contributing
Contributors
References
.md
.pdf
Contributing
Contributing
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