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AnnData(Set) object manipulation
snapatac2.AnnData
snapatac2.AnnData.X
snapatac2.AnnData.backend
snapatac2.AnnData.filename
snapatac2.AnnData.isbacked
snapatac2.AnnData.layers
snapatac2.AnnData.n_obs
snapatac2.AnnData.n_vars
snapatac2.AnnData.obs
snapatac2.AnnData.obs_names
snapatac2.AnnData.obsm
snapatac2.AnnData.obsp
snapatac2.AnnData.shape
snapatac2.AnnData.uns
snapatac2.AnnData.var
snapatac2.AnnData.var_names
snapatac2.AnnData.varm
snapatac2.AnnData.varp
snapatac2.AnnData.chunked_X
snapatac2.AnnData.close
snapatac2.AnnData.copy
snapatac2.AnnData.is_closed
snapatac2.AnnData.obs_ix
snapatac2.AnnData.open
snapatac2.AnnData.split_obs_by
snapatac2.AnnData.subset
snapatac2.AnnData.to_memory
snapatac2.AnnData.var_ix
snapatac2.AnnData.write
snapatac2.AnnDataSet
snapatac2.AnnDataSet.X
snapatac2.AnnDataSet.adatas
snapatac2.AnnDataSet.backend
snapatac2.AnnDataSet.isbacked
snapatac2.AnnDataSet.n_obs
snapatac2.AnnDataSet.n_vars
snapatac2.AnnDataSet.obs
snapatac2.AnnDataSet.obs_names
snapatac2.AnnDataSet.obsm
snapatac2.AnnDataSet.obsp
snapatac2.AnnDataSet.shape
snapatac2.AnnDataSet.uns
snapatac2.AnnDataSet.var
snapatac2.AnnDataSet.var_names
snapatac2.AnnDataSet.varm
snapatac2.AnnDataSet.varp
snapatac2.AnnDataSet.chunked_X
snapatac2.AnnDataSet.close
snapatac2.AnnDataSet.is_closed
snapatac2.AnnDataSet.obs_ix
snapatac2.AnnDataSet.split_obs_by
snapatac2.AnnDataSet.to_adata
snapatac2.AnnDataSet.var_ix
snapatac2.read
snapatac2.read_mtx
snapatac2.read_10x_mtx
snapatac2.read_dataset
snapatac2.concat
snapatac2.get_write_options
snapatac2.set_write_options
Preprocessing:
pp
snapatac2.pp.make_fragment_file
snapatac2.pp.import_fragments
snapatac2.pp.import_values
snapatac2.pp.import_contacts
snapatac2.pp.call_cells
snapatac2.pp.add_tile_matrix
snapatac2.pp.make_peak_matrix
snapatac2.pp.make_gene_matrix
snapatac2.pp.filter_cells
snapatac2.pp.select_features
snapatac2.pp.knn
snapatac2.pp.scrublet
snapatac2.pp.filter_doublets
snapatac2.pp.mnc_correct
snapatac2.pp.harmony
snapatac2.pp.scanorama_integrate
Tools:
tl
snapatac2.tl.spectral
snapatac2.tl.multi_spectral
snapatac2.tl.umap
snapatac2.tl.leiden
snapatac2.tl.kmeans
snapatac2.tl.dbscan
snapatac2.tl.hdbscan
snapatac2.tl.macs3
snapatac2.tl.merge_peaks
snapatac2.tl.marker_regions
snapatac2.tl.diff_test
snapatac2.tl.motif_enrichment
snapatac2.tl.init_network_from_annotation
snapatac2.tl.add_cor_scores
snapatac2.tl.add_regr_scores
snapatac2.tl.add_tf_binding
snapatac2.tl.link_tf_to_gene
snapatac2.tl.prune_network
snapatac2.tl.aggregate_X
snapatac2.tl.aggregate_cells
Metrics
snapatac2.metrics.frag_size_distr
snapatac2.metrics.tsse
snapatac2.metrics.frip
snapatac2.metrics.summary_by_chrom
Plotting:
pl
snapatac2.pl.tsse
snapatac2.pl.umap
snapatac2.pl.motif_enrichment
snapatac2.pl.regions
snapatac2.pl.coverage
snapatac2.pl.spectral_eigenvalues
snapatac2.pl.network_edge_stat
snapatac2.pl.render_plot
Exporting:
ex
snapatac2.ex.export_fragments
snapatac2.ex.export_coverage
Motif Analysis
snapatac2.PyDNAMotif
snapatac2.PyDNAMotif.family
snapatac2.PyDNAMotif.id
snapatac2.PyDNAMotif.name
snapatac2.PyDNAMotif.info_content
snapatac2.PyDNAMotif.with_nucl_prob
snapatac2.PyDNAMotifScanner
snapatac2.PyDNAMotifScanner.id
snapatac2.PyDNAMotifScanner.name
snapatac2.PyDNAMotifScanner.exist
snapatac2.PyDNAMotifScanner.exists
snapatac2.PyDNAMotifScanner.find
snapatac2.PyDNAMotifScanner.with_background
snapatac2.PyDNAMotifTest
snapatac2.PyDNAMotifTest.id
snapatac2.PyDNAMotifTest.name
snapatac2.PyDNAMotifTest.test
snapatac2.read_motifs
Datasets
snapatac2.genome.Genome
snapatac2.genome.Genome.annotation
snapatac2.genome.Genome.chrom_sizes
snapatac2.genome.Genome.fasta
snapatac2.genome.GRCh37
snapatac2.genome.GRCh38
snapatac2.genome.GRCm38
snapatac2.genome.GRCm39
snapatac2.genome.hg19
snapatac2.genome.hg38
snapatac2.genome.mm10
snapatac2.genome.mm39
snapatac2.datasets.cis_bp
snapatac2.datasets.Meuleman_2020
snapatac2.datasets.pbmc500
snapatac2.datasets.pbmc5k
snapatac2.datasets.pbmc10k_multiome
snapatac2.datasets.colon
snapatac2.datasets.cre_HEA
Recipes
snapatac2.pp.recipe_10x_metrics
API reference
Motif Analysis
snapatac2.PyDNAMotif
snapatac2.PyDNAMotif.name
snapatac2.PyDNAMotif.name
#
PyDNAMotif.
name
#
The name of the motif.
On this page
PyDNAMotif.name