API

• DonorData
  • cellink.DonorData
• Preprocessing pp
  • cellink.pp.variant_qc
  • cellink.pp.cell_level_obs_filter
  • cellink.pp.donor_level_obs_filter
  • cellink.pp.donor_level_var_filter
  • cellink.pp.log_transform
  • cellink.pp.low_abundance_filter
  • cellink.pp.missing_values_filter
  • cellink.pp.normalize
• Input-Output io
  • cellink.io.from_sgkit_dataset
  • cellink.io.read_plink
  • cellink.io.read_bgen
  • cellink.io.read_sgkit_zarr
  • cellink.io.read_pgen_zarr
  • cellink.io.stream_pgen_to_zarr
  • cellink.io.to_plink
  • cellink.io.write_variants_to_vcf
• Tools tl
  • cellink.tl.get_snp_df
  • cellink.tl.run_favor
  • cellink.tl.run_snpeff
  • cellink.tl.run_vep
  • cellink.tl.add_vep_annos_to_gdata
  • cellink.tl.combine_annotations
  • cellink.tl.aggregate_annotations_for_varm
  • cellink.tl.run_burden_test
  • cellink.tl.run_skat_test
  • cellink.tl.beta_weighting
• External tools tl.external
  • cellink.tl.external.calculate_ld
  • cellink.tl.external.run_jaxqtl
  • cellink.tl.external.read_jaxqtl_results
  • cellink.tl.external.run_mixmil
  • cellink.tl.external.calculate_pcs
  • cellink.tl.external.run_tensorqtl
  • cellink.tl.external.read_tensorqtl_results
  • cellink.tl.external.run_scdrs
  • cellink.tl.external.run_seismic
  • cellink.tl.external.run_magma_pipeline
  • cellink.tl.external.run_saigeqtl
  • cellink.tl.external.configure_saigeqtl_runner
  • cellink.tl.external.get_saigeqtl_runner
  • cellink.tl.external.make_group_file
  • cellink.tl.external.read_saigeqtl_results
  • cellink.tl.external.load_gsmap_results
  • cellink.tl.external.format_gsmap_sumstats
• Plotting
  • cellink.pl.locus
  • cellink.pl.manhattan
  • cellink.pl.qq
  • cellink.pl.expression_by_genotype
  • cellink.pl.volcano
• Machine Learning ml
  • cellink.ml.MILDataset
  • cellink.ml.mil_collate_fn
  • cellink.ml.DonorMILModel
• Association Testing at
  • cellink.at.acat_test
  • cellink.at.compute_acat
  • cellink.at.GWAS
  • cellink.at.Skat
• Utils
  • cellink.utils.column_normalize
  • cellink.utils.gaussianize
  • cellink.utils.one_hot_encode_genotypes
  • cellink.utils.dosage_per_strand
• Resources
  • cellink.resources.get_1000genomes
  • cellink.resources.get_1000genomes_grch38
  • cellink.resources.get_dummy_onek1k
  • cellink.resources.get_onek1k
  • cellink.resources.get_eqtl_catalog_dataset_associations
  • cellink.resources.get_eqtl_catalog_datasets
  • cellink.resources.get_gwas_catalog_studies
  • cellink.resources.get_gwas_catalog_study
  • cellink.resources.get_gwas_catalog_study_summary_stats
  • cellink.resources.get_pgs_catalog_score
  • cellink.resources.get_pgs_catalog_scores
  • cellink.resources.get_1000genomes_ld_scores
  • cellink.resources.get_1000genomes_ld_weights