Skip to main content
Ctrl
+
K
SnapATAC2 2.2.0 documentation
Site Navigation
Installation
Tutorials
API reference
Development
Learn
2.2
GitHub
Site Navigation
Installation
Tutorials
API reference
Development
Learn
2.2
GitHub
Section Navigation
Input/Output
snapatac2.AnnData
snapatac2.AnnData.X
snapatac2.AnnData.filename
snapatac2.AnnData.isbacked
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.subset
snapatac2.AnnData.to_memory
snapatac2.AnnData.var_ix
snapatac2.AnnData.write
snapatac2.AnnDataSet
snapatac2.AnnDataSet.X
snapatac2.AnnDataSet.adatas
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.copy
snapatac2.AnnDataSet.is_closed
snapatac2.AnnDataSet.obs_ix
snapatac2.AnnDataSet.subset
snapatac2.AnnDataSet.to_adata
snapatac2.AnnDataSet.var_ix
snapatac2.read
snapatac2.read_mtx
snapatac2.read_10x_mtx
snapatac2.read_csv
snapatac2.read_dataset
snapatac2.AnnData.write
snapatac2.AnnData.subset
snapatac2.AnnData.copy
snapatac2.AnnDataSet.subset
snapatac2.AnnDataSet.copy
Preprocessing:
pp
snapatac2.pp.make_fragment_file
snapatac2.pp.import_data
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.call_doublets
snapatac2.pp.mnc_correct
snapatac2.pp.harmony
Tools:
tl
snapatac2.tl.spectral
snapatac2.tl.laplacian
snapatac2.tl.umap
snapatac2.tl.leiden
snapatac2.tl.kmeans
snapatac2.tl.dbscan
snapatac2.tl.hdbscan
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.call_peaks
snapatac2.tl.aggregate_X
snapatac2.tl.aggregate_cells
Plotting:
pl
snapatac2.pl.tsse
snapatac2.pl.spectral_eigenvalues
snapatac2.pl.scrublet
snapatac2.pl.umap
snapatac2.pl.motif_enrichment
snapatac2.pl.regions
snapatac2.pl.network_edge_stat
snapatac2.pl.render_plot
Exporting:
ex
snapatac2.ex.export_bed
snapatac2.ex.export_bigwig
Datasets
snapatac2.genome.Genome
snapatac2.genome.Genome.fetch_annotations
snapatac2.genome.Genome.fetch_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.pbmc5k
snapatac2.datasets.pbmc_multiome
snapatac2.datasets.colon
snapatac2.datasets.cre_HEA
snapatac2.read_csv
#
snapatac2.
read_csv
(
csv_file
,
file
,
has_header
,
index_column
,
delimiter
,
/
)
#