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Main
Installation
API
scFates.pp.filter_cells
scFates.pp.batch_correct
scFates.pp.find_overdispersed
scFates.pp.diffusion
scFates.tl.tree
scFates.tl.curve
scFates.tl.circle
scFates.tl.cellrank_to_tree
scFates.tl.explore_sigma
scFates.tl.cleanup
scFates.tl.subset_tree
scFates.tl.attach_tree
scFates.tl.simplify
scFates.tl.convert_to_soft
scFates.tl.root
scFates.tl.roots
scFates.tl.pseudotime
scFates.tl.dendrogram
scFates.tl.test_association
scFates.tl.test_association_covariate
scFates.tl.test_association_monocle3
scFates.tl.fit
scFates.tl.cluster
scFates.tl.test_covariate
scFates.tl.linearity_deviation
scFates.tl.unroll_circle
scFates.tl.test_fork
scFates.tl.branch_specific
scFates.tl.activation
scFates.tl.activation_lm
scFates.tl.module_inclusion
scFates.tl.slide_cells
scFates.tl.slide_cors
scFates.tl.synchro_path
scFates.tl.synchro_path_multi
scFates.pl.graph
scFates.pl.trajectory
scFates.pl.trajectory_3d
scFates.pl.dendrogram
scFates.pl.milestones
scFates.pl.test_association
scFates.pl.single_trend
scFates.pl.trends
scFates.pl.matrix
scFates.pl.linearity_deviation
scFates.pl.binned_pseudotime_meta
scFates.pl.modules
scFates.pl.test_fork
scFates.pl.slide_cors
scFates.pl.synchro_path
scFates.pl.module_inclusion
scFates.get.fork_stats
scFates.get.modules
scFates.get.slide_cors
Release Notes
References
Walkthroughs
Basic Curved trajectory analysis
Tree analysis - Bone marrow fates
Tree operations
Exploring Sigma
Conversion from CellRank pipeline
Beyond scRNAseq: neuronal recordings
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