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Tutorials
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
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
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()