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Tutorials
DonorData basics: creating, syncing, slicing, and saving
Tutorial: Pseudobulk eQTL Analysis with
cellink
Tutorial: eQTL Analysis with JaxQTL and TensorQTL using
cellink
Tutorial: Annotating Genetic Variants with
cellink
Tutorial: Rare Variant Association Testing with
cellink
Tutorial: LD Clumping and Identifying Independent Signals with
cellink
Tutorial: Colocalization Analysis - Linking eQTLs to GWAS Signals with
cellink
Tutorial: Integrating GWAS with Single-Cell Data using cellink
Tutorial: Spatially Resolved GWAS Mapping with gsMap
Tutorial: eQTL Analysis with
SAIGE-QTL
using cellink
Tutorial: Using EHR Data as Donor-Level Input in
cellink
Tutorial: Using the
MILDataset
and PyTorch
DataLoader
in
cellink
Tutorial: Cell-Level LDSC analysis
Merging AnnData objects for cell-level LDSC (Duncan lab dataset)
Tutorial: MAGMA Gene-Set and Gene Property Analysis
Tutorial: sc-linker via cellink
Tutorial: Donor Effect Decomposition with LIVI using
cellink
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.read_dd
cellink.io.read_h5_dd
cellink.io.read_zarr_dd
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
cellink.tl.subset_genomic_region
cellink.tl.subset_gene
External tools
tl.external
cellink.tl.external.run_jaxqtl
cellink.tl.external.read_jaxqtl_results
cellink.tl.external.run_tensorqtl
cellink.tl.external.read_tensorqtl_results
cellink.tl.external.configure_saigeqtl_runner
cellink.tl.external.get_saigeqtl_runner
cellink.tl.external.make_group_file
cellink.tl.external.run_saigeqtl
cellink.tl.external.read_saigeqtl_results
cellink.tl.external.run_mixmil
cellink.tl.external.calculate_ld
cellink.tl.external.calculate_pcs
cellink.tl.external.configure_ldsc_runner
cellink.tl.external.munge_sumstats
cellink.tl.external.make_annot_from_bimfile
cellink.tl.external.make_annot_from_donor_data
cellink.tl.external.estimate_ld_scores_from_bimfile
cellink.tl.external.estimate_ld_scores_from_donor_data
cellink.tl.external.compute_ld_scores_with_annotations_from_bimfile
cellink.tl.external.compute_ld_scores_with_annotations_from_donor_data
cellink.tl.external.estimate_heritability
cellink.tl.external.estimate_celltype_specific_heritability
cellink.tl.external.estimate_genetic_correlation
cellink.tl.external.generate_gene_coord_file
cellink.tl.external.generate_sldsc_genesets
cellink.tl.external.get_magma_gene_loc
cellink.tl.external.preprocess_for_sldsc
cellink.tl.external.run_magma_pipeline
cellink.tl.external.run_magma_annotate
cellink.tl.external.run_magma_gene_analysis
cellink.tl.external.run_magma_gsa
cellink.tl.external.run_magma_gpa
cellink.tl.external.genesets_dir_to_entrez_gmt
cellink.tl.external.load_ensembl_to_entrez_map
cellink.tl.external.scores_to_gmt
cellink.tl.external.scores_to_covar
cellink.tl.external.format_gsmap_sumstats
cellink.tl.external.load_gsmap_results
cellink.tl.external.compute_celltype_programs
cellink.tl.external.compute_diseaseprogression_programs
cellink.tl.external.compute_nmf_programs
cellink.tl.external.compute_joint_nmf_programs
cellink.tl.external.JointNMFWrapper
cellink.tl.external.compute_escore
cellink.tl.external.run_sclinker_heritability
cellink.tl.external.compute_ld_scores_for_sclinker
cellink.tl.external.load_sclinker_heritability_results
cellink.tl.external.download_sclinker_references
cellink.tl.external.download_sclinker_enhancer_links
cellink.tl.external.load_roadmap_links
cellink.tl.external.load_abc_links
cellink.tl.external.load_gene_annotation
cellink.tl.external.genescores_to_abc_road_bedgraph
cellink.tl.external.genescores_to_100kb_bedgraph
cellink.tl.external.genescores_to_annotations
cellink.tl.external.bedgraph_to_snp_annotation
cellink.tl.external.check_and_patch_ldsc_parse_bug
cellink.tl.external.run_scdrs
cellink.tl.external.run_seismic
cellink.tl.external.run_seismic_torch
cellink.tl.external.SparseScore
cellink.tl.external.RegressionNLL
cellink.tl.external.prepare_scprs_data
cellink.tl.external.get_plink_commands_per_cell
cellink.tl.external.write_slurm_array_job
cellink.tl.external.get_disease_relevant_cells
cellink.tl.external.run_scprs_pipeline
cellink.tl.external.LIVIRunner
cellink.tl.external.configure_livi_runner
cellink.tl.external.get_livi_runner
cellink.tl.external.train_livi
cellink.tl.external.infer_livi
cellink.tl.external.run_livi_association_testing
cellink.tl.external.save_livi_results
cellink.tl.external.load_livi_results
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.liftover_gwas_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
cellink.resources.get_1000genomes_plink_files
cellink.resources.get_1000genomes_frq
cellink.resources.get_1000genomes_hapmap3
cellink.resources.merge_1000g_plink_chromosomes
PGEN → AnnData Conversion (
cellink-pgen
)
Changelog
Contributing guide
References
.rst
.pdf
cellink.tl.run_skat_test
Contents
run_skat_test()
cellink.tl.run_skat_test
#
cellink.tl.
run_skat_test
(
G
,
Y
,
F
,
gene
)
#
Contents
run_skat_test()