Skip to content

ME/CFS Biostatistics Home

analysis

Initializing search

ME/CFS Biostatistics Home

ME/CFS Biostatistics Home
Project Outline
Analysis
Analysis
- Alzheimers
  Alzheimers
  - Bellenguez et al 2022
    Bellenguez et al 2022
    
    MAGMA GTEx
    
    MAGMA HBA
    
    S-LDSC ALZ Analysis
- Asthma
  Asthma
  - Han et al 2020
    Han et al 2020
    
    cis-pQTL MR Analysis
    
    S-LDSC Asthma Analysis
- Brainstem
  Brainstem
  - Xue et al 2025
    Xue et al 2025
    
    MAGMA GTEx
    
    MAGMA HBA Analysis
    
    S-LDSC Analysis
- C Reactive Protein
  C Reactive Protein
  - Said et al
    Said et al
    
    LDSC
    
    MAGMA
    
    S-LDSC
- Diastolic Blood Pressure
  Diastolic Blood Pressure
  - Keaton et al 2024
    Keaton et al 2024
    
    MAGMA-GTEx Analysis
    
    MAGMA HBA Analysis
    
    S-LDSC DBP Analysis
- Education
  Education
  - Lee et al 2018
    Lee et al 2018
    
    MAGMA HBA Analysis
    
    MAGMA EDU Analysis
    
    S-LDSC EDU Analysis
- Epstein Barr
  Epstein Barr
  - Nyeo et al 2025
    Nyeo et al 2025
    
    MAGMA GTEx
    
    MAGMA HBA Analysis
    
    S-LDSC Analysis
- HHV7
  HHV7
  - Kamitaki et al 2025
    Kamitaki et al 2025
    
    MAGMA GTEx
    
    MAGMA HBA Analysis
    
    S-LDSC Analysis
- Heart
  Heart
  - Pirruccello et al 2022
    Pirruccello et al 2022
    
    S-LDSC Analysis of RVEF
    
    Master Gene List for RVEF
- Heart Rate Recovery
  Heart Rate Recovery
  - Verweiji et al 2018
    Verweiji et al 2018
    
    MAGMA GTEx
    
    HBA MAGMA
    
    S-LDSC
- Height
  Height
  - Yengo et al 2022
    Yengo et al 2022
    
    LDSC Analysis
- Inflammatory Bowel Disease
  Inflammatory Bowel Disease
  - Liu et al 2023
    Liu et al 2023
    
    MR with cis-pQTLs
    
    MAGMA HBA Analysis
    
    MAGMA IBD Analysis
    
    S-LDSC Analysis of IBD
- Low Density Lipoprotein
  Low Density Lipoprotein
  - Multistudy
    Multistudy
    
    Genetic Correlation
    Genetic Correlation
    
    CT-LDSC
  - Verma et al
    Verma et al
    
    LDL
    
    LDSC Analysis
    
    MAGMA Analysis of LDL
    
    S-LDSC LDL Analysis
  - Willer et al 2013
    Willer et al 2013
    
    LDSC
    
    MAGMA
    
    S-LDSC
- Lupus
  Lupus
  - Bentham et al 2025
    Bentham et al 2025
    
    MAGMA GTEx
    
    MAGMA HBA Analysis
    
    S-LDSC Analysis
- ME CFS
  ME CFS
  - DecodeME
    DecodeME
    
    Lead Variants
    
    Manhattan Plot
    
    Gene List
    
    Gene Set Analysis
    
    cis-pQTL MR Analysis
    
    LDSC
    
    MAGMA GTEx
    
    MAGMA HBA
    
    H-MAGMA
    
    S-LDSC
    
    Univariate MiXeR
    
    Fine Mapping
    Fine Mapping
    
    SUSIE
    SUSIE
    
    Chr1 173.5M-174.5M
    
    Chr6 26M-27M
    
    Chr6 97.5M-99M
    
    Chr15 54.5M-55.5M
    
    Chr17 50M-51M
    
    Chr20 47M-48.2M
    
    Specific Genes
    Specific Genes
    
    DCC
  - Million Veterans
    Million Veterans
    
    LDSC
    
    MAGMA
  - Multistudy
    Multistudy
    
    Genetic Correlation
    Genetic Correlation
    
    CT-LDSC
  - Neale Lab
    Neale Lab
    
    LDSC
    
    MAGMA
- Migraine
  Migraine
  - Verma et al
    Verma et al
    
    Migraine LDSC
- Multitrait
  Multitrait
  - Causal Inference
    Causal Inference
    
    LCV
    LCV
    
    Analysis of MI
  - Genetic Correlation
    Genetic Correlation
    
    CT-LDSC Study
  - Polygenic Overlap
    Polygenic Overlap
    
    Bivariate Mixer
    Bivariate Mixer
    
    DecodeME/Multisite Pain
- Pain
  Pain
  - Johnston et al 2019
    Johnston et al 2019
    
    Overview
    
    Gene-Level MAGMA
    
    MAGMA GTEx
    
    MAGMA HBA
    
    S-LDSC
    
    Univariate MiXeR
- RBC Volume
  RBC Volume
  - Verma et al
    Verma et al
    
    MAGMA Analysis of RBC Volume
    
    RBC Volume
    
    S-LDSC RBCV Analysis
- Schizophrenia
  Schizophrenia
  - PGC 2022
    PGC 2022
    
    MAGMA GTEx analysis
    
    MAGMA HBA Analysis
    
    S-LDSC Analysis of SCH
- Triglycerides
  Triglycerides
  - Willer et al 2013
    Willer et al 2013
    
    LDSC
    
    MAGMA
    
    S-LDSC
Bioinformatics Concepts
Bioinformatics Concepts
Codebase Concepts
Codebase Concepts
- Build System
- Figure System
Data Sources
Data Sources
Getting Started
Getting Started
API Reference
API Reference
- mecfs_bio
  mecfs_bio
  - mecfs_bio
  - analysis
    analysis
    
    analysis
    
    alzheimers
    
    asthma
    
    cfs_genetic_corr
    
    ct_ldsc_analysis
    
    dbp_analysis
    
    decode_me_fine_mapping
    
    decode_me_h_magma
    
    decode_me_initial_analysis
    
    heart_rate_recovery
    
    hhv7_analysis
    
    ibd_analysis
    
    johnston_multisite_pain_analysis
    
    ldl_analysis
    
    lee_educational_attainment_analysis
    
    lupus_analysis
    
    million_veterans_cfs_initial_analysis
    
    psoriasis_analysis
    
    pullit_body_fat_analysis
    
    red_blood_cell_volume
    
    ref_data
    
    right_heart_analysis
    
    schizophrenia_analysis
    
    syncope
    
    runner
    runner
    
    runner
    
    default_runner
  - asset_generator
    asset_generator
    
    asset_generator
    
    annovar_37_basic_rsid_assignment
    
    concrete_magma_asset_generator
    
    concrete_sldsc_generator
    
    concrete_standard_analysis_task_generator
    
    fine_mapping_asset_generator
    
    genetic_correlation_asset_generator
    
    h_magma_asset_generator
    
    hba_magma_asset_generator
    
    labeled_lead_variants_asset_generator
    
    lcv_asset_generator
    
    magma_curated_gene_set_analysis_generator
    
    mixer_asset_generator
    
    mr_with_cis_pqtl_asset_generator
    
    ukbb_broad_ld_matrix_generator
    
    ukbb_ppp_single_gwas_generator
  - assets
    assets
    
    assets
    
    executable
    executable
    
    executable
    
    extracted
    extracted
    
    extracted
    
    magma_binary_extracted
    
    raw
    raw
    
    raw
    
    magma_binary_zip
    
    gwas
    gwas
    
    gwas
    
    alzheimers
    alzheimers
    
    alzheimers
    
    bellenguez_et_al
    bellenguez_et_al
    
    bellenguez_et_al
    
    analysis
    analysis
    
    analysis
    
    bellenguez_standard_analysis
    
    processed
    processed
    
    processed
    
    extracted_bellinguez_data
    
    raw
    raw
    
    raw
    
    raw_bellenguez_data
    
    asthma
    asthma
    
    asthma
    
    han_et_al_2022
    han_et_al_2022
    
    han_et_al_2022
    
    analysis
    analysis
    
    analysis
    
    asthma_ppp_two_sample_mr_cis
    
    asthma_standard_analysis
    
    mr
    mr
    
    mr
    
    asthma_ppp_cis_mr_effect_measure_plot
    
    asthma_ppp_cis_mr_label_with_uniprot
    
    asthma_ppp_cis_mr_markdown
    
    asthma_ppp_cis_mr_multiple_testing
    
    asthma_ppp_cis_two_sample_mr_extract
    
    auxiliary
    auxiliary
    
    auxiliary
    
    prevalence_info
    
    raw
    raw
    
    raw
    
    raw_asthma_data
    
    blood_pressure
    blood_pressure
    
    blood_pressure
    
    keaton_et_al_diastolic
    keaton_et_al_diastolic
    
    keaton_et_al_diastolic
    
    analysis
    analysis
    
    analysis
    
    keaton_dbp_standard_analysis
    
    raw
    raw
    
    raw
    
    raw_dbp_data
    
    body_fat_distribution
    body_fat_distribution
    
    body_fat_distribution
    
    pullit_et_al_2018
    pullit_et_al_2018
    
    pullit_et_al_2018
    
    processed_gwas_data
    processed_gwas_data
    
    processed_gwas_data
    
    pullit_et_al_magma_task_generator
    
    raw_gwas_data
    raw_gwas_data
    
    raw_gwas_data
    
    pullit_et_al_raw_gwas_data
    
    brainstem
    brainstem
    
    brainstem
    
    whole_brainstem
    whole_brainstem
    
    whole_brainstem
    
    xue_et_al
    xue_et_al
    
    xue_et_al
    
    analysis
    analysis
    
    analysis
    
    xue_whole_brainstem_standard_analysis
    
    raw
    raw
    
    raw
    
    raw_xue_whole_brainstem
    
    c_reactive_protein
    c_reactive_protein
    
    c_reactive_protein
    
    said_et_al
    said_et_al
    
    said_et_al
    
    analysis
    analysis
    
    analysis
    
    said_crp_standard_analysis
    
    raw
    raw
    
    raw
    
    raw_crp_gwas_data
    
    ebv_dna
    ebv_dna
    
    ebv_dna
    
    nyeo_et_al
    nyeo_et_al
    
    nyeo_et_al
    
    analysis
    analysis
    
    analysis
    
    ebv_dna_standard_analysis
    
    raw
    raw
    
    raw
    
    ebv_dna
    
    educational_attainment
    educational_attainment
    
    educational_attainment
    
    lee_et_al_2018
    lee_et_al_2018
    
    lee_et_al_2018
    
    analysis
    analysis
    
    analysis
    
    hba_magma_analysis
    
    lee_et_al_edu_cis_pqtl_mr
    
    lee_et_al_h2_by_ldsc
    
    lee_et_al_standard_s_ldsc
    
    processed_gwas_data
    processed_gwas_data
    
    processed_gwas_data
    
    lee_et_al_magma_task_generator
    
    raw_gwas_data
    raw_gwas_data
    
    raw_gwas_data
    
    lee_et_al_catalog_harmonized
    
    heart_rate_recovery
    heart_rate_recovery
    
    heart_rate_recovery
    
    verweij_et_al_2018
    verweij_et_al_2018
    
    verweij_et_al_2018
    
    analysis
    analysis
    
    analysis
    
    verweiji_standard_analysis
    
    processed
    processed
    
    processed
    
    raw
    raw
    
    raw
    
    verweij_raw_summary
    
    height
    height
    
    height
    
    yengo_2022
    yengo_2022
    
    yengo_2022
    
    analysis
    analysis
    
    analysis
    
    yengo_standard_analysis
    
    raw
    raw
    
    raw
    
    yengo_height_raw
    
    human_herpesvirus_7_dna
    human_herpesvirus_7_dna
    
    human_herpesvirus_7_dna
    
    kamitaki_et_al_2025
    kamitaki_et_al_2025
    
    kamitaki_et_al_2025
    
    analysis
    analysis
    
    analysis
    
    kamitaki_et_al_2025_standard_analysis
    
    raw
    raw
    
    raw
    
    kamitaki_et_al_2025_raw
    
    imaging_derived_heart_phenotypes
    imaging_derived_heart_phenotypes
    
    imaging_derived_heart_phenotypes
    
    pirruccello_et_al_2022
    pirruccello_et_al_2022
    
    pirruccello_et_al_2022
    
    analysis
    analysis
    
    analysis
    
    rvef_standard_analysis
    
    processed
    processed
    
    processed
    
    extracted_rvef_data
    
    raw
    raw
    
    raw
    
    raw_right_heart_data
    
    inflammatory_bowel_disease
    inflammatory_bowel_disease
    
    inflammatory_bowel_disease
    
    liu_et_al_2023
    liu_et_al_2023
    
    liu_et_al_2023
    
    analysis
    analysis
    
    analysis
    
    cis_pqtl_mr
    
    liu_et_al_lead_variants
    
    liu_et_al_s_lsdc
    
    magma
    magma
    
    magma
    
    liu_et_al_2023_eur_37_hba_magma_analysis
    
    liu_et_al_2023_eur_37_magma_ensembl_specific_tisssue_gene_sets
    
    liu_et_al_2023_eur_37_specific_tissue_bar_plot
    
    auxiliary
    auxiliary
    
    auxiliary
    
    prevalence_nfo
    
    processed_gwas_data
    processed_gwas_data
    
    processed_gwas_data
    
    liu_et_al_2023_eur_37_harmonized_assign_rsid_via_snp150_annovar
    
    liu_et_al_2023_eur_37_harmonized_assign_rsid_via_snp150_annovar_with_dups
    
    liu_et_al_2023_eur_37_harmonized_assign_rsid_via_snp150_sumstats
    
    liu_et_al_2023_eur_37_harmonized_dump_to_parquet
    
    liu_et_al_2023_eur_37_harmonized_with_rsid_sumstats
    
    liu_et_al_2023_eur_liftover_to_37_parquet
    
    liu_et_al_2023_eur_liftover_to_37_sumstats
    
    liu_et_al_2023_eur_liftover_to_37_sumstats_harmonized
    
    liu_et_al_2023_eur_liftover_to_37_with_rsid
    
    liu_et_al_2023_eur_only
    
    magma
    magma
    
    magma
    
    liu_et_al_2023_eur_37_magma_ensembl_annotations
    
    liu_et_al_2023_eur_37_magma_ensembl_gene_analysis
    
    liu_et_al_2023_eur_37_magma_snp_locs
    
    liu_et_al_2023_eur_ibd_37_p_values
    
    raw_gwas_data
    raw_gwas_data
    
    raw_gwas_data
    
    liu_et_al_2023_meta
    
    ldl
    ldl
    
    ldl
    
    million_veterans
    million_veterans
    
    million_veterans
    
    analysis
    analysis
    
    analysis
    
    ldl_standard_sldsc
    
    million_veterans_ldl_eur_magma_task_generator
    
    mv_ldl_heritability_task
    
    auxiliary
    auxiliary
    
    auxiliary
    
    mv_ldl_pheotype_info
    
    processed_gwas_data
    processed_gwas_data
    
    processed_gwas_data
    
    raw_gwas_data
    raw_gwas_data
    
    raw_gwas_data
    
    raw_ldl_data
    
    multistudy
    multistudy
    
    multistudy
    
    genetic_correlation
    genetic_correlation
    
    genetic_correlation
    
    ct_ldsc
    ct_ldsc
    
    ct_ldsc
    
    ct_ldsc_ldl
    
    willer_et_al
    willer_et_al
    
    willer_et_al
    
    analysis
    analysis
    
    analysis
    
    willer_ldl_standard_analysis
    
    auxiliary
    auxiliary
    
    auxiliary
    
    willer_ldl_phenotype_info
    
    raw
    raw
    
    raw
    
    raw_willer_ldl_data
    
    me_cfs
    me_cfs
    
    me_cfs
    
    astra_zenica_phewas_gene_level
    astra_zenica_phewas_gene_level
    
    astra_zenica_phewas_gene_level
    
    raw
    raw
    
    raw
    
    get_mecfs_az_phewas
    
    decode_me
    decode_me
    
    decode_me
    
    analysis
    analysis
    
    analysis
    
    decode_me_gwas_1_cis_pqtl_mr
    
    decode_me_gwas_1_combined_gene_list_markdown
    
    decode_me_gwas_1_combined_gene_list_with_gget
    
    decode_me_gwas_1_combined_gene_lists
    
    decode_me_gwas_1_ldsc
    
    decode_me_gwas_1_lead_variant_region_plots
    
    decode_me_gwas_1_lead_variants
    
    decode_me_gwas_1_lead_variants_gene_labeled
    
    decode_me_gwas_1_manhattan
    
    decode_me_gwas_1_manhattan_and_qq
    
    decode_me_region_plot_BTN1A1_locus_37
    
    decode_me_region_plot_rabgap1l_locus_37
    
    decode_me_sldsc
    
    fine_mapping
    fine_mapping
    
    fine_mapping
    
    with_palindromes
    with_palindromes
    
    with_palindromes
    
    susie_finemap_decode_me_37_chr15_54_925_638_locus_plalindindromes
    
    susie_finemap_decode_me_37_chr17_50_237_377_locus_palindromes
    
    susie_finemap_decode_me_37_chr1_174_128_548_locus_palindromes
    
    susie_finemap_decode_me_37_chr20_47_653_230_locus_palindromes
    
    susie_finemap_decode_me_37_chr6_26_215_000_locus_palindromes
    
    susie_finemap_decode_me_37_chr6_97_505_620_locus_palindromes
    
    without_palindromes
    without_palindromes
    
    without_palindromes
    
    susie_finemap_decode_me_37_chr15_54_925_638_locus
    
    susie_finemap_decode_me_37_chr17_50_237_377_locus
    
    susie_finemap_decode_me_37_chr1_173_locus
    
    susie_finemap_decode_me_37_chr1_173_locus_stackplot
    
    susie_finemap_decode_me_37_chr20_47_653_230_locus
    
    susie_finemap_decode_me_37_chr6_26_215_000_locus
    
    susie_finemap_decode_me_37_chr6_97_505_620_locus
    
    h_magma
    h_magma
    
    h_magma
    
    decode_me_h_magma_asset_generator
    
    magma
    magma
    
    magma
    
    decode_me_curated_gene_set_analysis
    
    decode_me_filtered_gene_list
    
    decode_me_filtered_gene_list_with_gene_metadata
    
    decode_me_filtered_gene_list_with_gene_metadata_drop_cols
    
    decode_me_gwas_1_build_37_entrez_gsea_hallmark_gene_sets
    
    decode_me_gwas_1_build_37_magma_ensembl_specific_tissue_gene_sets
    
    decode_me_gwas_1_build_37_magma_ensembl_specific_tissue_gene_sets_brain_average
    
    decode_me_hba_magma_analysis
    
    decode_me_magma_gene_plot
    
    decode_me_magma_gene_plot_with_window
    
    magma_specific_tissue_bar_plot
    
    magma_specific_tissue_bar_plot_brain_average
    
    mixer
    mixer
    
    mixer
    
    decode_me_univariate_mixer
    
    auxiliary
    auxiliary
    
    auxiliary
    
    prevalance_info
    
    processed_gwas_data
    processed_gwas_data
    
    processed_gwas_data
    
    decode_me_annovar_37_rsids_assignment
    
    decode_me_gwas_1_37_parquet_file
    
    decode_me_gwas_1_annovar_37_sumstats
    
    decode_me_gwas_1_build_37_with_rsid
    
    decode_me_gwas_1_sumstats_liftover_to_37
    
    decode_me_gwas_1_sumstats_minimal_processing
    
    decode_me_with_annovar_37_rsids_sumstats
    
    filtered_snps_gwas_1
    
    magma
    magma
    
    magma
    
    decode_me_gwas_1_build_37_magma_ensembl_annotations
    
    decode_me_gwas_1_build_37_magma_ensembl_annotations_with_window
    
    decode_me_gwas_1_build_37_magma_ensembl_gene_analysis
    
    decode_me_gwas_1_build_37_magma_ensembl_gene_analysis_with_window
    
    decode_me_gwas_1_build_37_magma_entrez_annotations
    
    decode_me_gwas_1_build_37_magma_entrez_gene_analysis
    
    decode_me_gwas_1_build_37_magma_snp_locs
    
    decode_me_gwas_1_build_37_magma_snp_p_values
    
    prep_for_fine_mapping
    prep_for_fine_mapping
    
    prep_for_fine_mapping
    
    chr1_173_locus
    chr1_173_locus
    
    chr1_173_locus
    
    harmonize_with_polyfun_reference_alleles
    
    harmonize_with_polyfun_reference_rsid
    
    raw_gwas_data
    raw_gwas_data
    
    raw_gwas_data
    
    decode_me_gwas_1
    
    decode_me_quality_control_snps
    
    decode_me_female
    decode_me_female
    
    decode_me_female
    
    analysis
    analysis
    
    analysis
    
    decode_me_female_standard_analysis
    
    auxiliary
    auxiliary
    
    auxiliary
    
    decode_me_female_phenotype_info
    
    processed
    processed
    
    processed
    
    filtered_snps_decode_me_female
    
    raw
    raw
    
    raw
    
    decode_me_female_raw
    
    decode_me_gwas_2
    decode_me_gwas_2
    
    decode_me_gwas_2
    
    analysis
    analysis
    
    analysis
    
    decode_me_gwas_2_standard_analysis
    
    auxiliary
    auxiliary
    
    auxiliary
    
    decode_me_gwas_2_phenotype_info
    
    processed
    processed
    
    processed
    
    filtered_snps_decode_me_gwas_2
    
    raw
    raw
    
    raw
    
    decode_me_gwas_2_raw
    
    decode_me_infectious_onset
    decode_me_infectious_onset
    
    decode_me_infectious_onset
    
    analysis
    analysis
    
    analysis
    
    decode_me_infectious_onset_standard_analysis
    
    auxiliary
    auxiliary
    
    auxiliary
    
    decode_me_infectious_onset_phenotype_info
    
    processed
    processed
    
    processed
    
    filtered_snps_decode_me_infectious_onset
    
    raw
    raw
    
    raw
    
    decode_me_infectious_onset_raw
    
    decode_me_male
    decode_me_male
    
    decode_me_male
    
    analysis
    analysis
    
    analysis
    
    decode_me_male_standard_analysis
    
    auxiliary
    auxiliary
    
    auxiliary
    
    decode_me_male_phenotype_info
    
    processed
    processed
    
    processed
    
    filtered_snps_decode_me_male
    
    raw
    raw
    
    raw
    
    decode_me_male_raw
    
    decode_me_non_infectious_onset
    decode_me_non_infectious_onset
    
    decode_me_non_infectious_onset
    
    analysis
    analysis
    
    analysis
    
    decode_me_non_infectious_onset_standard_analysis
    
    auxiliary
    auxiliary
    
    auxiliary
    
    decode_me_non_infectious_onset_phenotype_info
    
    processed
    processed
    
    processed
    
    filtered_snps_decode_me_non_infectious_onset
    
    raw
    raw
    
    raw
    
    decode_me_non_infectious_onset_raw
    
    million_veterans
    million_veterans
    
    million_veterans
    
    analysis
    analysis
    
    analysis
    
    million_veterans_cfs_standard_analysis
    
    auxiliary
    auxiliary
    
    auxiliary
    
    pheotype_info
    
    raw
    raw
    
    raw
    
    million_veterans_cfs_download
    
    multistudy
    multistudy
    
    multistudy
    
    analysis
    analysis
    
    analysis
    
    genetic_correlation
    genetic_correlation
    
    genetic_correlation
    
    ct_ldsc
    ct_ldsc
    
    ct_ldsc
    
    ct_ldsc_mecfs_studies
    
    ct_ldsc_mecfs_studies_plot
    
    neale_lab
    neale_lab
    
    neale_lab
    
    analysis
    analysis
    
    analysis
    
    neale_lab_cfs_standard_analysis
    
    auxiliary
    auxiliary
    
    auxiliary
    
    neale_lab_cfs_phenotype_info
    
    processed
    processed
    
    processed
    
    neale_lab_cfs_gwas_joined
    
    raw
    raw
    
    raw
    
    neale_lab_cfs_gwas_download
    
    migraine
    migraine
    
    migraine
    
    million_veterans
    million_veterans
    
    million_veterans
    
    analysis
    analysis
    
    analysis
    
    million_veterans_migraine_standard_analysis
    
    raw
    raw
    
    raw
    
    million_veterans_migraine_raw
    
    multi_trait
    multi_trait
    
    multi_trait
    
    genetic_correlation
    genetic_correlation
    
    genetic_correlation
    
    ct_ldsc
    ct_ldsc
    
    ct_ldsc
    
    ct_ldsc_initial_asset_generator
    
    ct_ldsc_plot
    
    mi_willer_ldl_correlation
    
    lava
    lava
    
    lava
    
    initial_lava
    
    genomic_sem
    genomic_sem
    
    genomic_sem
    
    lcv
    lcv
    
    lcv
    
    ldl_mi_lcv_analysis
    
    mecf_pain_lcv_analysis
    
    mi_lcv_analysis
    
    polygenic_overlap
    polygenic_overlap
    
    polygenic_overlap
    
    bivariate_mixer
    bivariate_mixer
    
    bivariate_mixer
    
    mecfs_pain_bivariate_mixer
    
    multisite_pain
    multisite_pain
    
    multisite_pain
    
    johnston_et_al
    johnston_et_al
    
    johnston_et_al
    
    analysis
    analysis
    
    analysis
    
    johnston_standard_analysis
    
    magma
    magma
    
    magma
    
    johnston_gene_level_magma_plot
    
    mixer
    mixer
    
    mixer
    
    johnston_et_al_univariate_mixer
    
    auxiliary
    auxiliary
    
    auxiliary
    
    sample_info
    
    processed
    processed
    
    processed
    
    extracted_johnston_data
    
    raw
    raw
    
    raw
    
    raw_johnston_data
    
    myocardial_infarction
    myocardial_infarction
    
    myocardial_infarction
    
    analysis
    analysis
    
    analysis
    
    mi_standard_analysis
    
    raw
    raw
    
    raw
    
    raw_mi_data
    
    psoriasis
    psoriasis
    
    psoriasis
    
    million_veterans
    million_veterans
    
    million_veterans
    
    analysis
    analysis
    
    analysis
    
    processed_gwas_data
    processed_gwas_data
    
    processed_gwas_data
    
    million_veterans_psoriasis_eur_magma_task_generator
    
    raw_gwas_data
    raw_gwas_data
    
    raw_gwas_data
    
    raw_psoriasis_data
    
    red_blood_cell_volume
    red_blood_cell_volume
    
    red_blood_cell_volume
    
    million_veterans
    million_veterans
    
    million_veterans
    
    analysis
    analysis
    
    analysis
    
    rbc_vol_sldsc
    
    rbc_volume_magma_task_generator
    
    raw_gwas_data
    raw_gwas_data
    
    raw_gwas_data
    
    raw_red_blood_volume
    
    schizophrenia
    schizophrenia
    
    schizophrenia
    
    pgc2022
    pgc2022
    
    pgc2022
    
    analysis
    analysis
    
    analysis
    
    sch_clustermap_plot
    
    magma
    magma
    
    magma
    
    pgc2022_sch_magma_human_brain_atlas
    
    pgc2022_sch_magma_human_brain_atlas_conditional_analysis
    
    pgc2022_sch_magma_human_brain_atlas_plot
    
    pgc2022_sch_magma_human_brain_atlas_results_extract
    
    pgc2022_sch_magma_human_brain_atlas_results_labeled
    
    pgc2022_sch_magma_human_brain_atlas_results_multiple_testing
    
    pgc_2022_magma_hba_spec_matrix_filtered
    
    pgc_2022_sch_human_brain_atlas_stepwise_plot
    
    pgc_2022_sch_magma_human_brain_atlas_forward_stepwise
    
    drg
    drg
    
    drg
    
    auxiliary
    auxiliary
    
    auxiliary
    
    prevalance_info
    
    processed
    processed
    
    processed
    
    standard_analysis_sc_pgc_2022
    
    magma
    magma
    
    magma
    
    pgc2022_sch_entrez_annotations
    
    pgc2022_sch_magna_entrez_gene_analysis
    
    raw
    raw
    
    raw
    
    raw_sch_pgc2022
    
    syncope
    syncope
    
    syncope
    
    aegisdottir_et_al
    aegisdottir_et_al
    
    aegisdottir_et_al
    
    analysis
    analysis
    
    analysis
    
    syncope_hba_magma_task_generator
    
    syncope_magma_task_generator
    
    syncope_s_ldsc
    
    auxiliary
    auxiliary
    
    auxiliary
    
    prevelnce_info
    
    processed
    processed
    
    processed
    
    sumstats_liftover_dump_to_parquet
    
    syncope_sumstats_explode_and_scale
    
    syncope_sumstats_liftover
    
    syncope_sumstats_liftover_hapmap3_dedup
    
    raw
    raw
    
    raw
    
    raw_syncope_data
    
    systemic_lupus_erythematosus
    systemic_lupus_erythematosus
    
    systemic_lupus_erythematosus
    
    bentham_et_al_2015
    bentham_et_al_2015
    
    bentham_et_al_2015
    
    analysis_results
    analysis_results
    
    analysis_results
    
    bentham_2015_gene_sets
    
    bentham_2015_raw_37_lead_variant_region_plots
    
    bentham_2015_raw_37_lead_variants
    
    bentham_2015_standard_analysis
    
    auxiliary
    auxiliary
    
    auxiliary
    
    prevalence_info
    
    processed_gwas_data
    processed_gwas_data
    
    processed_gwas_data
    
    bentham_2015_harmonized_sumstats_minimal_processing
    
    bentham_2015_raw_sumstats_minimal_processing
    
    raw_gwas_data
    raw_gwas_data
    
    raw_gwas_data
    
    bentham_2015_raw_build_37
    
    raw_gwas_data_harmonized
    raw_gwas_data_harmonized
    
    raw_gwas_data_harmonized
    
    bentham_2015_harmonized_build_38
    
    triglycerides
    triglycerides
    
    triglycerides
    
    willer_et_al
    willer_et_al
    
    willer_et_al
    
    analysis
    analysis
    
    analysis
    
    triglycide_standard_analysis
    
    raw
    raw
    
    raw
    
    raw_triglyceride_data
    
    ukbb_ppp
    ukbb_ppp
    
    ukbb_ppp
    
    btn1a1
    btn1a1
    
    btn1a1
    
    generator
    generator
    
    generator
    
    retrieve_and_process
    
    raw
    raw
    
    raw
    
    rabgap1l
    rabgap1l
    
    rabgap1l
    
    analysis
    analysis
    
    analysis
    
    fine_mapping
    fine_mapping
    
    fine_mapping
    
    prep_for_fine_mapping
    prep_for_fine_mapping
    
    prep_for_fine_mapping
    
    chr1_173_locus
    chr1_173_locus
    
    chr1_173_locus
    
    processed
    processed
    
    processed
    
    raw
    raw
    
    raw
    
    reference_data
    reference_data
    
    reference_data
    
    db_snp
    db_snp
    
    db_snp
    
    db_sn150_build_37_annovar_proc_parquet
    
    db_sn150_build_37_annovar_proc_parquet_rename
    
    db_sn150_build_37_annovar_proc_parquet_rename_unique
    
    db_snp150_build_37_annovar_proc
    
    db_snp_build_37_as_parquet
    
    db_snp_build_37_as_parquet_unnest_ref
    
    db_snp_build_37_as_parquet_unnest_ref_sorted
    
    db_snp_vcf_file_for_rsid_assignment_build_37
    
    db_snp_vcf_file_with_index
    
    snp151_build37_parquet
    
    snp151_build_37
    
    ensembl_biomart
    ensembl_biomart
    
    ensembl_biomart
    
    gene_thesaurus
    
    gene_set_data
    gene_set_data
    
    gene_set_data
    
    for_magma
    for_magma
    
    for_magma
    
    from_fuma
    from_fuma
    
    from_fuma
    
    gtex_v8_tissue_type_gene_sets
    
    from_gsea_msigdb
    from_gsea_msigdb
    
    from_gsea_msigdb
    
    auxiliary
    auxiliary
    
    auxiliary
    
    extracted
    extracted
    
    extracted
    
    full_msigdb_sqlite_extracted
    
    gsea_entrez_human_gene_set_2025_v1_extracted
    
    processed
    processed
    
    processed
    
    full_msigdb_parquet_from_sqlite
    
    raw
    raw
    
    raw
    
    full_msigdb_sqlite_zipped
    
    gsea_entrez_human_gene_set_2025_v1
    
    genomic_sem_reference
    genomic_sem_reference
    
    genomic_sem_reference
    
    genomes_1k
    
    hapmap3_snpist
    
    h_magma_annotations
    h_magma_annotations
    
    h_magma_annotations
    
    raw
    raw
    
    raw
    
    adult_brain_h_magma_annot
    
    cortical_neuron_h_magma_annot
    
    fetal_brain_h_magma_annot
    
    ipsc_derived_astro_h_magma_annot
    
    ipsc_derived_neuro_h_magma_annot
    
    midbrain_da_h_magma_annot
    
    human_brain_atlas
    human_brain_atlas
    
    human_brain_atlas
    
    raw
    raw
    
    raw
    
    cluster_annotation_term_metadata
    
    lava
    lava
    
    lava
    
    lava_ld_reference
    lava_ld_reference
    
    lava_ld_reference
    
    g1000_eur
    g1000_eur
    
    g1000_eur
    
    processed
    processed
    
    processed
    
    lava_thousand_geomes_eur_ld_ref_extracted
    
    raw
    raw
    
    raw
    
    thousand_genomes_eur_ld_ref
    
    ukbb
    ukbb
    
    ukbb
    
    raw
    raw
    
    raw
    
    ukbb_lava_ld_ref
    
    lava_locus_file
    lava_locus_file
    
    lava_locus_file
    
    default
    default
    
    default
    
    raw
    raw
    
    raw
    
    default_lava_locus_file
    
    lava_vignette_data
    lava_vignette_data
    
    lava_vignette_data
    
    lava_vignette_data
    
    laval_locus_definitions
    laval_locus_definitions
    
    laval_locus_definitions
    
    raw
    raw
    
    raw
    
    linkage_disequilibrium_score_reference_data
    linkage_disequilibrium_score_reference_data
    
    linkage_disequilibrium_score_reference_data
    
    custom
    custom
    
    custom
    
    roadmap_cell_type_categorization
    
    extracted
    extracted
    
    extracted
    
    eur_ld_scores_thousand_genome_phase_3_v1_extracted
    
    eur_ld_scores_thousand_genomes_phase_3_v1_consolidated
    
    partitioned_model_cahoy_ld_scores_extracted
    
    partitioned_model_corces_atac_ld_scores_extracted
    
    partitioned_model_gtex_brain_ld_scores_extracted
    
    partitioned_model_immgen_ld_scores_extracted
    
    partitioned_model_multi_tissue_chromatin_ld_scores_extracted
    
    partitioned_model_multi_tissue_gene_expr_ld_score_extracted
    
    partitioned_model_regression_weights_extracted
    
    thousand_genome_baseline_ld_extracted
    
    from_papers
    from_papers
    
    from_papers
    
    finucane_2018_franke_gtex_categories
    
    finucane_2018_immgen_categories
    
    raw
    raw
    
    raw
    
    eur_ld_scores_thousand_genome_phase_3_v1_raw
    
    partitioned_model_allele_freq
    
    partitioned_model_baseline_ld_scores
    
    partitioned_model_cahoy_ld_scores
    
    partitioned_model_corces_atac
    
    partitioned_model_gtex_brain_ld_scores
    
    partitioned_model_immgen_ld_scores
    
    partitioned_model_multi_tissue_chromatin_ld_scores
    
    partitioned_model_multi_tissue_gene_expr_ld_scores
    
    partitioned_model_regression_weights
    
    magma_gene_locations
    magma_gene_locations
    
    magma_gene_locations
    
    processed
    processed
    
    processed
    
    magma_entrez_gene_locations_data_build_37_unzipped
    
    raw
    raw
    
    raw
    
    magma_ensembl_gene_location_reference_data_build_37
    
    magma_entrez_gene_location_reference_data_build_37
    
    magma_entrez_gene_location_reference_data_build_38
    
    magma_ld_reference
    magma_ld_reference
    
    magma_ld_reference
    
    magma_eur_build_37_1k_genomes_ref_extracted
    
    magma_eur_build_37_1k_genomes_ref_raw
    
    magma_specificity_matrices
    magma_specificity_matrices
    
    magma_specificity_matrices
    
    processed
    processed
    
    processed
    
    curated_potential_mecfs_gene_sets_specificity_matrix
    
    curated_potential_mecfs_gene_sets_specificity_matrix_reduced
    
    raw
    raw
    
    raw
    
    magma_specificity_matrix_from_hbca_rna_duncan
    
    mixer
    mixer
    
    mixer
    
    hello_world
    hello_world
    
    hello_world
    
    mixer_hello_world_data
    
    processed
    processed
    
    processed
    
    mixer_g1000_plink_eur_extracted
    
    raw
    raw
    
    raw
    
    mixer_g1000_plink_eur_raw
    
    neale_lab_reference_data
    neale_lab_reference_data
    
    neale_lab_reference_data
    
    neale_lab_phenotype_summary_file
    
    neale_lab_variant_list
    
    pqtls
    pqtls
    
    pqtls
    
    processed
    processed
    
    processed
    
    sun_et_al_2023_pqtls_combined_extracted
    
    sun_et_al_2023_pqtls_discovery_extracted
    
    raw
    raw
    
    raw
    
    sun_et_al_2023_pqtls
    
    research_paper_supplementary_material
    research_paper_supplementary_material
    
    research_paper_supplementary_material
    
    duncan_et_al_2025
    duncan_et_al_2025
    
    duncan_et_al_2025
    
    processed
    processed
    
    processed
    
    duncan_et_al_2025_st1_extracted
    
    duncan_et_al_2025_st1_label_columns
    
    raw
    raw
    
    raw
    
    duncan_et_al_2025_supplementary_raw
    
    rna_seq_data
    rna_seq_data
    
    rna_seq_data
    
    gtex
    gtex
    
    gtex
    
    gtex_v10_median_tissue_expression_rna_seq_extracted
    
    gtex_v10_median_tissue_expression_rna_seq_prep_for_magma
    
    gtex_v10_median_tissue_expression_rna_seq_prep_for_magma_brain_average
    
    gtex_v10_median_tissue_expression_rna_seq_raw
    
    yu_drg
    yu_drg
    
    yu_drg
    
    processed
    processed
    
    processed
    
    yu_drg_cepo_specificity_matrix
    
    yu_drg_counts_long
    
    yu_drg_counts_long_with_cell_type
    
    yu_drg_extracted_counts_data
    
    yu_drg_extracted_counts_with_ensemlb_gene_names
    
    yu_drg_frac_specificity_matrix
    
    raw
    raw
    
    raw
    
    yu_drg_metadata_table
    
    yu_drg_raw_counts_rdata
    
    ukbb_ld_matrices
    ukbb_ld_matrices
    
    ukbb_ld_matrices
    
    from_polyfun
    from_polyfun
    
    from_polyfun
    
    chr1_173000001
    chr1_173000001
    
    chr1_173000001
    
    chr1_173000001_176000001_labels
    
    chr1_173000001_176000001_matrix
    
    chr_1_174000001
    chr_1_174000001
    
    chr_1_174000001
    
    chr1_174000001_177000001_labels
    
    chr1_174000001_177000001_matrix
    
    ukbb_ppp_sumstats
    ukbb_ppp_sumstats
    
    ukbb_ppp_sumstats
    
    rabgap1l
    rabgap1l
    
    rabgap1l
    
    analysis
    analysis
    
    analysis
    
    ukbb_rabgap1l_region_plot_37
    
    processed
    processed
    
    processed
    
    stack_ukbb_rabgap1l
    
    ukbb_rabgap1l_sumstats_37
    
    untar_ukbb_rabgap_1l
    
    raw
    raw
    
    raw
    
    ukbb_ppp_rabgap1l
    
    uniprot
    uniprot
    
    uniprot
    
    uniprot_lookup_table
  - build_system
    build_system
    
    build_system
    
    asset
    asset
    
    asset
    
    base_asset
    
    directory_asset
    
    file_asset
    
    data_manipulation
    data_manipulation
    
    data_manipulation
    
    xr_data
    xr_data
    
    xr_data
    
    xr_gene_dataset
    
    xr_gene_dataset_load
    
    xr_gene_specificity_heatmap
    
    meta
    meta
    
    meta
    
    asset_id
    
    base_meta
    
    executable_meta
    
    filtered_gwas_data_meta
    
    gwas_summary_file_meta
    
    markdown_file_meta
    
    meta
    
    plot_file_meta
    
    plot_meta
    
    processed_gwas_data_directory_meta
    
    result_directory_meta
    
    result_table_meta
    
    simple_directory_meta
    
    simple_file_meta
    
    gwaslab_meta
    gwaslab_meta
    
    gwaslab_meta
    
    gwaslab_lead_variants_meta
    
    gwaslab_manhattan_plot_meta
    
    gwaslab_region_plots_meta
    
    gwaslab_sumstats_meta
    
    read_spec
    read_spec
    
    read_spec
    
    dataframe_read_spec
    
    read_dataframe
    
    read_path
    
    read_spec
    
    read_sumstats
    
    reference_meta
    reference_meta
    
    reference_meta
    
    reference_data_directory_meta
    
    reference_file_meta
    
    rebuilder
    rebuilder
    
    rebuilder
    
    base_rebuilder
    
    sandboxed_execute
    
    tracking_sandboxed_execute
    
    fetch
    fetch
    
    fetch
    
    base_fetch
    
    restricted_fetch
    
    metadata_to_path
    metadata_to_path
    
    metadata_to_path
    
    base_meta_to_path
    
    simple_meta_to_path
    
    verifying_trace_rebuilder
    verifying_trace_rebuilder
    
    verifying_trace_rebuilder
    
    verifying_trace_info
    
    verifying_trace_rebuilder_core
    
    tracer
    tracer
    
    tracer
    
    base_tracer
    
    imohash
    
    simple_hasher
    
    reference
    reference
    
    reference
    
    nc_chrom_mapping
    
    schemas
    schemas
    
    schemas
    
    chrom_rename_rules
    
    hg19_sn151_schema
    
    hg19_snp151_schema_valid_choms
    
    runner
    runner
    
    runner
    
    info_purge
    
    simple_runner
    
    scheduler
    scheduler
    
    scheduler
    
    asset_retrieval
    
    topological_scheduler
    
    serialization
    serialization
    
    serialization
    
    converter
    
    task
    task
    
    task
    
    assign_rsids_via_snp151_task
    
    base_task
    
    combine_gene_lists_task
    
    compressed_csv_to_parquet_task
    
    concat_frames_in_dir_task
    
    concat_frames_task
    
    consolidate_ld_scores_task
    
    convert_dataframe_to_markdown_task
    
    copy_file_from_directory_task
    
    copy_task
    
    counting_task
    
    discard_deps_task_wrapper
    
    download_file_task
    
    download_files_into_directory_task
    
    download_from_google_drive_task
    
    external_directory_copy_task
    
    external_file_copy_task
    
    extract_all_from_zip_task
    
    extract_dataframe_from_rdata_task
    
    extract_gzip_task
    
    extract_sheet_from_excel_file_task
    
    extract_tar_gzip_task
    
    extraction_one_file_from_zip_task
    
    failing_task
    
    fake_task
    
    fetch_gget_info_task
    
    filter_snps_task
    
    fixed_effect_meta_analysis_task
    
    gene_manhattan_plot_task
    
    gene_tissue_expression_clustermap_task
    
    genetic_correlation_clustermap_task
    
    get_file_from_synapse_task
    
    get_uniprot_reference_data_task
    
    harmonize_gwas_with_reference_table_via_chrom_pos_alleles
    
    harmonize_gwas_with_reference_table_via_rsid
    
    join_dataframes_task
    
    lava_task
    
    make_executable_wrapper_task
    
    multiple_testing_table_task
    
    osf_retrieve_task
    
    pipe_dataframe_task
    
    plot_mr_effect_measure_task
    
    specificity_cepo_task
    
    specificity_frac_task
    
    sqlite_to_parquet_task
    
    susie_stacked_plot_task
    
    two_sample_mr_task
    
    upset_plot_task
    
    gwaslab
    gwaslab
    
    gwaslab
    
    gwaslab_cell_analysis_by_sldsc
    
    gwaslab_create_sumstats_task
    
    gwaslab_genetic_corr_by_ct_ldsc_task
    
    gwaslab_lead_variants_task
    
    gwaslab_manhattan_and_qq_plot_task
    
    gwaslab_region_plot_task_arbitrary_locus
    
    gwaslab_region_plots_task
    
    gwaslab_snp_heritability_by_ldsc_task
    
    gwaslab_sumstats_to_table_task
    
    gwaslab_transform_sumstats
    
    gwaslab_util
    
    sldsc_scatter_plot_task
    
    lcv
    lcv
    
    lcv
    
    lcv_clustermap
    
    lcv_core
    
    lcv_task
    
    magma
    magma
    
    magma
    
    magma_annotate_task
    
    magma_forward_stepwise_select_task
    
    magma_gene_analysis_task
    
    magma_gene_set_analysis_task
    
    magma_plot_brain_atlas_result_with_stepwise_labels
    
    magma_plot_gene_set_result
    
    magma_snp_location_task
    
    magma_subset_specificity_matrix_using_top_labels
    
    plot_magma_brain_atlas_result
    
    prepare_gene_sets_for_magma_task
    
    mixer
    mixer
    
    mixer
    
    bivariate_mixer_task
    
    bivariate_mixer_test_task
    
    mixer_bivariate_combine
    
    mixer_bivariate_results
    
    mixer_task
    
    mixer_univariate_combine
    
    mixer_univariate_results
    
    mixer_utils
    
    pipes
    pipes
    
    pipes
    
    add_average_pipe
    
    cast_pipe
    
    composite_pipe
    
    compute_beta_pipe
    
    compute_mlog10p_pipe
    
    compute_p_from_beta_se
    
    compute_p_pipe
    
    compute_se_pipe
    
    concat_str_pipe
    
    data_processing_pipe
    
    drop_col_pipe
    
    drop_null_pipe
    
    duckdb_mem_limit_pipe
    
    filter_rows_by_info_score
    
    filter_rows_by_min
    
    filter_rows_by_min_in_col
    
    filter_rows_by_value
    
    format_numbers_pipe
    
    head_pipe
    
    heritability_conversion_pipe
    
    identity_pipe
    
    join_with_memory_table_pipe
    
    log_markdown_pipe
    
    max_with_constant_pipe
    
    move_col_to_front_pipe
    
    pivot_pipe
    
    rename_col_by_position_pipe
    
    rename_col_pipe
    
    replace_pipe
    
    scale_col_pipe
    
    select_pipe
    
    set_col_pipe
    
    shifted_log_pipe
    
    sort_pipe
    
    str_lowercase_pipe
    
    str_replace_pipe
    
    str_split_col
    
    str_split_exact_col
    
    to_polars_pipe
    
    transpose_pipe
    
    uniquepipe
    
    unnest_pipe
    
    unpivot_pipe
    
    winsorize_all
    
    r_tasks
    r_tasks
    
    r_tasks
    
    susie_r_finemap_task
    
    genomic_sem
    genomic_sem
    
    genomic_sem
    
    xr_pipes
    xr_pipes
    
    xr_pipes
    
    xr_cluster
    
    xr_composite
    
    xr_data_pipe
    
    xr_identity
    
    xr_most_significant
    
    xr_significance_filter
    
    task_generator
    task_generator
    
    task_generator
    
    magma_task_generator
    
    master_gene_list_task_generator
    
    sldsc_task_generator
    
    tasks
    tasks
    
    tasks
    
    base_tasks
    
    simple_tasks
    
    wf
    wf
    
    wf
    
    base_wf
  - constants
    constants
    
    constants
    
    genomic_coordinate_constants
    
    gh_constants
    
    gwaslab_constants
    
    magma_constants
    
    msigdb_columns
    
    sun_et_al_pqtl_constants
    
    uniprot_constants
    
    xr_constants
    
    curated_gene_set_collections
    curated_gene_set_collections
    
    curated_gene_set_collections
    
    curated_mecfs_gene_sets
    
    reduced_curated_mecfs_gene_sets
    
    vocabulary_classes
    vocabulary_classes
    
    vocabulary_classes
    
    gene_set
    
    genomic_interval
  - figures
    figures
    
    figures
    
    fig_constants
    
    figure_exporter
    
    figure_task_list
    
    manifest
    
    manifest_validation
    
    orphan_pruning
    
    key_scripts
    key_scripts
    
    key_scripts
    
    generate_figures
    
    generate_new_figures
    
    prune_orphan_figures
    
    publish_figures
    
    pull_figures
    
    push_figures
    
    regenerate_figures
    
    validate_manifest
  - vend_files
    vend_files
    
    vend_files

mecfs_bio.assets.gwas.migraine.million_veterans.analysis

Modules:

million_veterans_migraine_standard_analysis –

Made with Material for MkDocs