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decode_me_minus_pain
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ME/CFS Biostatistics Home
GitHub
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
Heart
Heart
Pirruccello et al 2022
Pirruccello et al 2022
Master Gene List for RVEF
S-LDSC Analysis of 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
HHV7
HHV7
Kamitaki et al 2025
Kamitaki et al 2025
MAGMA GTEx
MAGMA HBA Analysis
S-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
Note on Phenotype
LDSC
MAGMA
Multistudy
Multistudy
Genetic Correlation
Genetic Correlation
CT-LDSC
Neale Lab
Neale Lab
LDSC
MAGMA
Migraine
Migraine
UK BioBank 2025
UK BioBank 2025
Overview
MAGMA GTEx
MAGMA HBA
S-LDSC
LDSC
Verma et al
Verma et al
LDSC
Multitrait
Multitrait
Causal Inference
Causal Inference
LCV
LCV
Analysis of MI
Genetic Correlation
Genetic Correlation
CT-LDSC Study
GenomicSEM
GenomicSEM
GWAS By Subtracton
GWAS By Subtracton
DecodeME Minus Multsite Pain
DecodeME Minus Multsite Pain
Overview
Genetic Correlation
MAGMA
MAGMA GTEx
MAGMA HBA
H-MAGMA
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
H MAGMA
RA
RA
DECODE (Seronegative)
DECODE (Seronegative)
Overview
S-LDSC
MAGMA (GTEx)
LDSC
MAGMA (HBA)
DECODE (Seropositive)
DECODE (Seropositive)
Overview
S-LDSC
MAGMA (GTEx)
LDSC
MAGMA (HBA)
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
CT-LDSC
Epigenetics
Fine Mapping
Genetic Correlation
GWAS by Subtraction
Heritability
LDSC
MAGMA
Mendelian Randomization
MiXeR
Omnigenic Model
S-LDSC
Sumstats Standardization
Codebase Concepts
Codebase Concepts
Build System
Figure System
Data Sources
Data Sources
Corces et al. Blood Cell Epigenetics
DecodeME
GTEx Bulk RNA-seq
HBA scRNA-seq
ImmGen
Million Veterans Program
Roadmap Epigenetics Project
UK Biobank
UKBB PPP
Getting Started
Getting Started
Initial Setup
Standard Workflow
Synapse
Adding Packages
Experiments Directory
Docker
Reference
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
decode_me_pain_subtraction_ols
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
uk_biobank_2025_migraine_analysis
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
ukbb_ppp_slim_protein_asset_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
processed
processed
processed
acat_az_phewas
pivoted_az_phewas
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_lead_variants_markdown
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
build_38
build_38
build_38
decode_me_build_38_s_ldsc
build_38_s_ldsc_export
build_38_s_ldsc_export
build_38_s_ldsc_export
build_38_roadmap_add_modaility
build_38_s_ldsc_all_tables
build_38_s_ldsc_all_tables_bonferroni
build_38_s_ldsc_all_tables_fdr
fine_mapping
fine_mapping
fine_mapping
with_palindromes
with_palindromes
with_palindromes
susie_finemap_decode_me_37_chr1_174_128_548_locus_palindromes
susie_finemap_decode_me_37_chr6_26_215_000_locus_palindromes
susie_finemap_decode_me_37_chr6_97_505_620_locus_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_chr20_47_653_230_locus_palindromes
without_palindromes
without_palindromes
without_palindromes
susie_finemap_decode_me_37_chr1_173_locus
susie_finemap_decode_me_37_chr1_173_locus_stackplot
susie_finemap_decode_me_37_chr6_26_215_000_locus
susie_finemap_decode_me_37_chr6_97_505_620_locus
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_chr20_47_653_230_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
decode_me_magma_gene_table_markdown
magma_specific_tissue_bar_plot
magma_specific_tissue_bar_plot_brain_average
mixer
mixer
mixer
decode_me_univariate_mixer
s_ldsc_export
s_ldsc_export
s_ldsc_export
decode_me_sldsc_all_tables
decode_me_sldsc_all_tables_bonferroni
decode_me_sldsc_all_tables_combined
decode_me_sldsc_all_tables_fdr
decode_me_sldsc_roadmap_add_modality_column
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
build_38
build_38
build_38
decode_me_gwas_1_assign_rsids_build_38
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_minus_pain
decode_me_minus_pain
decode_me_minus_pain
analysis
analysis
analysis
residual_genetic_corr_ols
standard_analysis_decodeme_minus_pain_ols
raw
raw
raw
decode_me_minus_pain_ols_extract
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
uk_biobank_2025
uk_biobank_2025
uk_biobank_2025
analysis
analysis
analysis
uk_biobank_2025_migraine_standard_analysis
processed
processed
processed
uk_biobank_2025_migraine_common_snps
raw
raw
raw
uk_biobank_2025_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
decode_me_minus_pain_subtraction_ols
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
rheumtoid_arthritis
rheumtoid_arthritis
rheumtoid_arthritis
decode_seronegative
decode_seronegative
decode_seronegative
analysis
analysis
analysis
ra_seronegative_standard_analysis
processed
processed
processed
ra_seronegative_preprocess
raw
raw
raw
download_raw_ra_seronegative
decode_seropositive
decode_seropositive
decode_seropositive
analysis
analysis
analysis
ra_seropositive_standard_analysis
processed
processed
processed
ra_seropositive_preprocess
raw
raw
raw
download_raw_ra_seropositive
util
util
util
decode_cohort_sample_sizes
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
ppp_database
ppp_database
ppp_database
hapmap3
hapmap3
hapmap3
hapmap3_ppp_database_protein_files
hapmap3_ppp_membership_list
hapmap_3_ppp_index
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_build_37
db_snp_vcf_file_with_index_build_38
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
thousand_genomes
thousand_genomes
thousand_genomes
common_1kg_variants_eur_hg38
eur_hg38_30x_vcf
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
regenerate_ppp_manifest
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
sample_size_spec
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_archive_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
gc_post_execute_hook
info_purge
simple_runner
scheduler
scheduler
scheduler
asset_retrieval
topological_scheduler
serialization
serialization
serialization
converter
task
task
task
acat_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_files_into_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_by_frequency
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
whitespace_sep_text_to_parquet_task
zip_dir_task
gwaslab
gwaslab
gwaslab
gwaslab_assign_rsids_via_sweep_task
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
effective_n_from_cohort_string_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
ppp_database
ppp_database
ppp_database
allele_key
build_slim_protein_parquet_task
byte_stream_split_parquet
common_1kg_membership_task
construct_ppp_variant_index_task
filter_common_1kg_variants_task
hapmap3_membership_task
r_tasks
r_tasks
r_tasks
susie_r_finemap_task
genomic_sem
genomic_sem
genomic_sem
genomic_sem_gwas_by_subtraction_full_python_task
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
synapse_downloader
wf_downloader
constants
constants
constants
genomic_coordinate_constants
gh_constants
gwaslab_constants
ldsc_constants
magma_constants
msigdb_columns
ppp_index_constants
regenie_constants
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.me_cfs.decode_me_minus_pain
Modules:
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