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SnapATAC2 2.3.1 documentation

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  • Installation
  • Tutorials
  • API reference
  • Development
  • Learn

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  • Input/Output
    • 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.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.subset
      • snapatac2.AnnDataSet.to_adata
      • snapatac2.AnnDataSet.var_ix
    • snapatac2.read
    • snapatac2.read_mtx
    • snapatac2.read_dataset
    • snapatac2.AnnData.write
    • snapatac2.AnnData.subset
    • snapatac2.AnnData.copy
    • snapatac2.AnnDataSet.subset
  • Preprocessing: pp
    • snapatac2.pp.make_fragment_file
    • snapatac2.pp.import_data
    • snapatac2.pp.add_frip
    • 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
  • 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.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.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.Meuleman_2020
    • snapatac2.datasets.pbmc500
    • snapatac2.datasets.pbmc5k
    • snapatac2.datasets.pbmc10k_multiome
    • snapatac2.datasets.colon
    • snapatac2.datasets.cre_HEA
  • API reference
  • Datasets
  • snapatac2.genome.Genome

snapatac2.genome.Genome#

class snapatac2.genome.Genome(chrom_sizes, annotation_filename, fasta=None)[source]#

Methods

fetch_annotations()

fetch_fasta()

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Datasets

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snapatac2.genome.Genome.fetch_annotations
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  • Genome

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