From 5eeb54627f1b8e30246242057036940cb02b3430 Mon Sep 17 00:00:00 2001 From: Anjing Liu Date: Sun, 21 Jun 2026 22:06:05 -0700 Subject: [PATCH 1/3] Update flowchart: fix data flow connections and colocboost link MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Add Step 3 (geno/pheno/cov-prep) → Step 5b connections for individual-level fine-mapping methods (SuSiE/mvSuSiE/fSuSiE) - Add section descriptions to each pipeline stage card - Fix ColocBoost wiki link to pecotmr_integration/colocboost.html - Split Gene Expression into Bulk and Pseudobulk parallel tracks - Various badge and layout fixes Co-Authored-By: Claude Sonnet 4.6 --- xqtl_flowchart.html | 21 ++++++++++++--------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/xqtl_flowchart.html b/xqtl_flowchart.html index 7402863c..d4141224 100644 --- a/xqtl_flowchart.html +++ b/xqtl_flowchart.html @@ -289,8 +289,8 @@

FunGen-xQTL Computational Protocol

+ data-out="cov-prep,qtl-assoc,fine-map" + data-tip="Inputs: variant annotations ← Reference Data Outputs: formatted genotypes → QTL Testing; genotype PCs → Covariate Preprocessing; individual genotypes → Fine-mapping (mvSuSiE/fSuSiE)">
🧪
Step 3a
Genotype Preprocessing
QC raw VCF, convert to PLINK, filter by HWE/missingness, compute kinship and genotype PCs
@@ -321,8 +321,8 @@

FunGen-xQTL Computational Protocol

+ data-out="cov-prep,qtl-assoc,fine-map" + data-tip="Inputs: raw phenotype matrices ← Molecular Phenotypes Outputs: phenotype BED files → QTL Testing; phenotype data → Covariate Preprocessing; individual phenotypes → Fine-mapping (mvSuSiE/fSuSiE)">
📊
Step 3b
Phenotype Preprocessing
Annotate genomic coordinates, impute missing values, and reformat phenotype matrices into BED files for QTL testing
@@ -347,8 +347,8 @@

FunGen-xQTL Computational Protocol

+ data-out="qtl-assoc,fine-map" + data-tip="Inputs: genotype PCs ← Genotype Preprocessing; phenotype data ← Phenotype Preprocessing Outputs: covariate files (PCs + hidden factors) → QTL Testing; covariates → Fine-mapping (SuSiE/mvSuSiE/fSuSiE)">
🔧
Step 3c
Covariate Preprocessing
Merge genotype PCs with phenotypic covariates, then estimate hidden confounders (PEER / Marchenko PCA)
@@ -432,9 +432,9 @@

FunGen-xQTL Computational Protocol

+ data-tip="Inputs: summary stats ← QTL Testing; mixture priors ← MASH; individual genotypes, phenotypes & covariates ← Step 3 (for SuSiE/mvSuSiE/fSuSiE) Outputs: credible sets + PIPs + TWAS weights → GWAS Integration, Enrichment, EMS">
🎯
Step 5b
Multiomics Regression / Fine-mapping
Pinpoint causal variants within QTL loci using Bayesian credible sets (SuSiE, mvSuSiE, RSS) and generate TWAS weights
@@ -489,7 +489,7 @@

FunGen-xQTL Computational Protocol

MWETWAS & cTWAS Gene-level trait association using expression weights - + MWEColocBoost Shared-variant discovery across molecular traits @@ -574,6 +574,9 @@

FunGen-xQTL Computational Protocol

['cov-prep', 'qtl-assoc', 'covariate files', '#0f766e'], ['qtl-assoc', 'mash', 'per-context effect sizes', '#b45309'], ['qtl-assoc', 'fine-map', 'nominal summary stats', '#b45309'], + ['geno-prep', 'fine-map', 'individual genotypes (SuSiE/mvSuSiE/fSuSiE)', '#1d4ed8'], + ['pheno-prep', 'fine-map', 'individual phenotypes (SuSiE/mvSuSiE/fSuSiE)', '#0891b2'], + ['cov-prep', 'fine-map', 'covariates (SuSiE/mvSuSiE/fSuSiE)', '#0f766e'], ['mash', 'fine-map', 'mixture priors (mvSuSiE)', '#1e40af'], ['fine-map', 'gwas-integ', 'credible sets + TWAS weights', '#be123c'], ['fine-map', 'enrich', 'fine-mapped variants', '#be123c'], From 211ce7a54749a7ca9fed1510a7e3e9e2fa869403 Mon Sep 17 00:00:00 2001 From: Anjing Liu Date: Sun, 21 Jun 2026 22:23:57 -0700 Subject: [PATCH 2/3] Fix tooltip text to include SuSiE alongside mvSuSiE/fSuSiE Co-Authored-By: Claude Sonnet 4.6 --- xqtl_flowchart.html | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/xqtl_flowchart.html b/xqtl_flowchart.html index d4141224..3e7663ad 100644 --- a/xqtl_flowchart.html +++ b/xqtl_flowchart.html @@ -290,7 +290,7 @@

FunGen-xQTL Computational Protocol

+ data-tip="Inputs: variant annotations ← Reference Data Outputs: formatted genotypes → QTL Testing; genotype PCs → Covariate Preprocessing; individual genotypes → Fine-mapping (SuSiE/mvSuSiE/fSuSiE)">
🧪
Step 3a
Genotype Preprocessing
QC raw VCF, convert to PLINK, filter by HWE/missingness, compute kinship and genotype PCs
@@ -322,7 +322,7 @@

FunGen-xQTL Computational Protocol

+ data-tip="Inputs: raw phenotype matrices ← Molecular Phenotypes Outputs: phenotype BED files → QTL Testing; phenotype data → Covariate Preprocessing; individual phenotypes → Fine-mapping (SuSiE/mvSuSiE/fSuSiE)">
📊
Step 3b
Phenotype Preprocessing
Annotate genomic coordinates, impute missing values, and reformat phenotype matrices into BED files for QTL testing
From 762a23da460e0122bc1fca3db420444de1631feb Mon Sep 17 00:00:00 2001 From: Anjing Liu Date: Sun, 21 Jun 2026 22:56:35 -0700 Subject: [PATCH 3/3] =?UTF-8?q?Fix=20flowchart:=20add=20qtl-assoc=E2=86=92?= =?UTF-8?q?gwas-integ=20for=20ColocBoost;=20clarify=20GWAS=20sumstats=20in?= =?UTF-8?q?put?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit ColocBoost uses QTL sumstats (QtlDataset RDS) directly, not GWAS sumstats — add the missing qtl-assoc→gwas-integ connection. Also correct the ref-data→gwas-integ label from "LD reference + gene annotations" to "GWAS sumstats + LD reference" since SuSiE-enloc and cTWAS require external GWAS sumstats as their primary input. Co-Authored-By: Claude Sonnet 4.6 --- xqtl_flowchart.html | 23 +++++++++++++---------- 1 file changed, 13 insertions(+), 10 deletions(-) diff --git a/xqtl_flowchart.html b/xqtl_flowchart.html index 3e7663ad..f7e6e5ce 100644 --- a/xqtl_flowchart.html +++ b/xqtl_flowchart.html @@ -175,8 +175,8 @@

FunGen-xQTL Computational Protocol

+ data-out="mol-pheno,geno-prep,fine-map,gwas-integ,enrich" + data-tip="Outputs: ref genome & annotations → Molecular Phenotypes; variant annotations → Genotype Preprocessing; LD reference → Fine-mapping (RSS); LD + gene annotations → GWAS Integration; LD scores → Enrichment (S-LDSC)">
📚
Step 1
Reference Data
Reference genome, gene annotations, LD matrices, and TADB boundaries shared across all downstream steps
@@ -374,8 +374,8 @@

FunGen-xQTL Computational Protocol

+ data-out="mash,gwas-integ" + data-tip="Inputs: formatted genotypes + phenotype BED + covariate files Outputs: per-context effect sizes & SEs → MASH; QTL sumstats → GWAS Integration (ColocBoost)">
⚡
Step 4
QTL Association Testing
Scan all variant–phenotype pairs (cis & trans) with TensorQTL, then apply hierarchical multiple-testing correction
@@ -432,9 +432,9 @@

FunGen-xQTL Computational Protocol

+ data-tip="Inputs: individual genotypes, phenotypes & covariates ← Step 3 (SuSiE/mvSuSiE/fSuSiE); mixture priors ← MASH (mvSuSiE); LD reference ← Reference Data (RSS) Outputs: credible sets + PIPs + TWAS weights → GWAS Integration, Enrichment, EMS">
🎯
Step 5b
Multiomics Regression / Fine-mapping
Pinpoint causal variants within QTL loci using Bayesian credible sets (SuSiE, mvSuSiE, RSS) and generate TWAS weights
@@ -473,9 +473,9 @@

FunGen-xQTL Computational Protocol

+ data-tip="Inputs: credible sets, PIPs, TWAS weights ← Fine-mapping; GWAS sumstats, LD reference & gene annotations ← Reference Data; QTL sumstats ← QTL Association (ColocBoost) Outputs: colocalization posteriors, gene associations → Enrichment">
🔗
Step 6
GWAS Integration
Link QTL signals to GWAS loci via colocalization (SuSiE-enloc, ColocBoost) and gene-level associations (TWAS / cTWAS)
@@ -503,7 +503,7 @@

FunGen-xQTL Computational Protocol

📉
@@ -573,12 +573,15 @@

FunGen-xQTL Computational Protocol

['pheno-prep', 'qtl-assoc', 'phenotype BED files', '#0891b2'], ['cov-prep', 'qtl-assoc', 'covariate files', '#0f766e'], ['qtl-assoc', 'mash', 'per-context effect sizes', '#b45309'], - ['qtl-assoc', 'fine-map', 'nominal summary stats', '#b45309'], ['geno-prep', 'fine-map', 'individual genotypes (SuSiE/mvSuSiE/fSuSiE)', '#1d4ed8'], ['pheno-prep', 'fine-map', 'individual phenotypes (SuSiE/mvSuSiE/fSuSiE)', '#0891b2'], ['cov-prep', 'fine-map', 'covariates (SuSiE/mvSuSiE/fSuSiE)', '#0f766e'], + ['ref-data', 'fine-map', 'LD reference (RSS)', '#7c3aed'], ['mash', 'fine-map', 'mixture priors (mvSuSiE)', '#1e40af'], ['fine-map', 'gwas-integ', 'credible sets + TWAS weights', '#be123c'], + ['ref-data', 'gwas-integ', 'GWAS sumstats + LD reference', '#7c3aed'], + ['qtl-assoc', 'gwas-integ', 'QTL sumstats (ColocBoost)', '#b45309'], + ['ref-data', 'enrich', 'LD scores (S-LDSC)', '#7c3aed'], ['fine-map', 'enrich', 'fine-mapped variants', '#be123c'], ['fine-map', 'ems', 'variant features', '#be123c'], ['gwas-integ', 'enrich', 'colocalization posteriors', '#7e22ce'],