Docs polish: workflow builder updates, link and citation fixes, writing style by jaempawi · Pull Request #1440 · StatFunGen/xqtl-protocol

Home page: plain intro, correct NIAGADS link, in-site Environment Setup link, named links instead of bare URLs

jaempawi

committed

2482892

Builder: point SuSiE-enloc notes to the current mnm_regression and rss_analysis notebooks; README: NIAGADS as plain text

jaempawi

committed

ea63dc6

Builder: add LeafCutter2 splicing calling and QTL summary-statistics fine-mapping and TWAS weights (replaces the placeholder); remove retired GRM, ld_reference_generation, METAL_pipeline and pseudo…

jaempawi

committed

4a61a58

Builder text: no em dashes, US spelling throughout (colocalization, normalize, analyze), Reference Preparation label

jaempawi

committed

8fdd04c

Builder: scEEMS Prediction available (model path .cbm), main page heading, larger buttons and links, form first on phones; use joint fine-mapping in the builder and fine-mapping pages

jaempawi

committed

f791baf

Docs: no em dashes, US spelling, hyphenated fine-mapping, headings without colons, METAL notes and VCF QC intro rewritten, typo fixes

jaempawi

committed

951c111

Docs: US spelling in seven notebooks and the builder (reorganized, initialization, behavior, relabeled, modeling, analyzing, center, standardizes, labeling)

jaempawi

committed

526994b

Docs: fix moved and dead links, correct two citation labels, rewrite spaced hyphens used as dashes, US spelling, logo alt text

jaempawi

committed

a65f21e

Label links to private lab repositories on protocol site pages

jaempawi

committed

79c671c

Docs: fix review findings (tau vs enrichment, reference-data links, LD pruning wording, METAL weighting, fixture size, missXGBoost, redact a cached HPC path, builder heading order and dashes)

jaempawi

committed

cea9a35

scEEMS Prediction: mark as not yet available (predict step is a stub); builder shows the coming-soon sign

jaempawi

committed

06da17f

Restore multivariate fine-mapping wording; fine-mapping vignettes write outputs under output/<workflow>/ like the other pages

jaempawi

committed

5fc8e79

METAL sample-size mode uses square-root-of-N weights; scEEMS Prediction text says the module is not yet available

jaempawi

committed

c5f5db5

scEEMS output filenames match the R worker; softer environment claim on the demo page; leave code comments unchanged

jaempawi

committed

6224bcf

Miniprotocol timing headings at level 2 (no skipped heading levels); McArthur et al. 2021 DOI link without URL encoding

jaempawi

committed

eda581c

Builder: timing shows a valid duration (no NaN for modules timed as text); detail panel fits the phone screen as a bottom sheet; link back to the protocol home page

jaempawi

committed

12b473c

Univariate fine-mapping vignette lists the region manifest the command writes (susie_twas_region_manifest.tsv)

jaempawi

committed

9408abe

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Docs polish: workflow builder updates, link and citation fixes, writing style - #1440

Docs polish: workflow builder updates, link and citation fixes, writing style#1440
jaempawi wants to merge 17 commits into
StatFunGen:mainfrom
jaempawi:readme-polish-nov10

Commits on Nov 10, 2026

Home page: plain intro, correct NIAGADS link, in-site Environment Setup link, named links instead of bare URLs

Builder: point SuSiE-enloc notes to the current mnm_regression and rss_analysis notebooks; README: NIAGADS as plain text

Builder: add LeafCutter2 splicing calling and QTL summary-statistics fine-mapping and TWAS weights (replaces the placeholder); remove retired GRM, ld_reference_generation, METAL_pipeline and pseudo…

Builder text: no em dashes, US spelling throughout (colocalization, normalize, analyze), Reference Preparation label

Builder: scEEMS Prediction available (model path .cbm), main page heading, larger buttons and links, form first on phones; use joint fine-mapping in the builder and fine-mapping pages

Docs: no em dashes, US spelling, hyphenated fine-mapping, headings without colons, METAL notes and VCF QC intro rewritten, typo fixes

Docs: US spelling in seven notebooks and the builder (reorganized, initialization, behavior, relabeled, modeling, analyzing, center, standardizes, labeling)

Docs: fix moved and dead links, correct two citation labels, rewrite spaced hyphens used as dashes, US spelling, logo alt text

Label links to private lab repositories on protocol site pages

Docs: fix review findings (tau vs enrichment, reference-data links, LD pruning wording, METAL weighting, fixture size, missXGBoost, redact a cached HPC path, builder heading order and dashes)

scEEMS Prediction: mark as not yet available (predict step is a stub); builder shows the coming-soon sign

Restore multivariate fine-mapping wording; fine-mapping vignettes write outputs under output/<workflow>/ like the other pages

METAL sample-size mode uses square-root-of-N weights; scEEMS Prediction text says the module is not yet available

scEEMS output filenames match the R worker; softer environment claim on the demo page; leave code comments unchanged

Miniprotocol timing headings at level 2 (no skipped heading levels); McArthur et al. 2021 DOI link without URL encoding

Builder: timing shows a valid duration (no NaN for modules timed as text); detail panel fits the phone screen as a bottom sheet; link back to the protocol home page

Univariate fine-mapping vignette lists the region manifest the command writes (susie_twas_region_manifest.tsv)