diff --git a/.code_reader/auditor_backlog.md b/.code_reader/auditor_backlog.md
index d6625af..11e68af 100644
--- a/.code_reader/auditor_backlog.md
+++ b/.code_reader/auditor_backlog.md
@@ -1,10 +1,10 @@
# Auditor Backlog — ctdR
-Exported: 2026-06-15T17:44:31.509210
+Exported: 2026-06-17T21:47:52.604138
## R/import_CTD.R
-- **.save_ctd_cache** (function, L167-192)
+- **.save_ctd_cache** (function, L245-267) [TO REVIEW]
## R/utils-input.R
diff --git a/.code_reader/review_manifest.json b/.code_reader/review_manifest.json
index adb178c..6afa68a 100644
--- a/.code_reader/review_manifest.json
+++ b/.code_reader/review_manifest.json
@@ -2,15 +2,287 @@
"project": {
"name": "ctdR",
"path": "/Users/lcorsaro/Documents/Progetti/RICERCA/ctdR/ctdR",
- "total": 1188,
- "read": 5,
- "unread": 1183,
- "needs_re_review": 0,
- "completion_pct": 0.4,
- "last_sync": "2026-06-16T11:17:28.871640",
- "last_scan_commit": "1f5bedd68f946ffd085d84533430db9c7fbffc7d"
+ "total": 1261,
+ "read": 4,
+ "unread": 1256,
+ "needs_re_review": 1,
+ "completion_pct": 0.3,
+ "last_sync": "2026-06-17T21:47:52.613629",
+ "last_scan_commit": "a0d9f40d6ae3cea4b0f8682ac618d0d416443941"
},
"units": [
+ {
+ "qualified_name": ".coding_agent/2026-06-15_session.md::section::Session diary — 2026-06-15",
+ "file_path": ".coding_agent/2026-06-15_session.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "467c890e24a48c2c",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-15_session.md::section::Cosa è stato fatto",
+ "file_path": ".coding_agent/2026-06-15_session.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "080879b743b1f616",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-15_session.md::section::vignette (`ctdR.Rmd`) — ORA real-data section",
+ "file_path": ".coding_agent/2026-06-15_session.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "8765215682240a33",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-15_session.md::section::manuscript (`paper.tex` + `paper.pdf`)",
+ "file_path": ".coding_agent/2026-06-15_session.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "5940e35c40f61d2c",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-15_session.md::section::Backlog",
+ "file_path": ".coding_agent/2026-06-15_session.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "e1ed256a637c67a7",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-15_session.md::section::Decisioni prese e perché",
+ "file_path": ".coding_agent/2026-06-15_session.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "d44334aabc4ca789",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-15_session.md::section::Cosa rimane aperto",
+ "file_path": ".coding_agent/2026-06-15_session.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "927d245fb9f19930",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-15_session.md::section::Blocchi / dipendenze",
+ "file_path": ".coding_agent/2026-06-15_session.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "409c5bf131237691",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-16_session.md::section::Session diary — 2026-06-16",
+ "file_path": ".coding_agent/2026-06-16_session.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "cd207a31a0502e8b",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-16_session.md::section::Cosa è stato fatto",
+ "file_path": ".coding_agent/2026-06-16_session.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "a9f841a14711af7c",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-16_session.md::section::Package (branch feat/interaction-filter-universe → PR #34 → merged)",
+ "file_path": ".coding_agent/2026-06-16_session.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "2992a44820120f43",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-16_session.md::section::Tutorial (vignettes/articles/tutorial_rnaseq_workflow.Rmd)",
+ "file_path": ".coding_agent/2026-06-16_session.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "dc657855b5cf19f2",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-16_session.md::section::Paper (manuscript/)",
+ "file_path": ".coding_agent/2026-06-16_session.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "4b9d48b7852303fe",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-16_session.md::section::Review Stanford",
+ "file_path": ".coding_agent/2026-06-16_session.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "0e99ae7c8346d1af",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-16_session.md::section::PR e release",
+ "file_path": ".coding_agent/2026-06-16_session.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "f28d7d37ab1d418a",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-16_session.md::section::Decisioni prese",
+ "file_path": ".coding_agent/2026-06-16_session.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "c8f317d7d4445c08",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-16_session.md::section::Post-chiusura (addendum)",
+ "file_path": ".coding_agent/2026-06-16_session.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "a237f4e88a8bfb8f",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-16_session.md::section::Cosa rimane aperto",
+ "file_path": ".coding_agent/2026-06-16_session.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "73405247a63cd5e3",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-17_session.md::section::Session diary — 2026-06-17",
+ "file_path": ".coding_agent/2026-06-17_session.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "2cc950402c6529d3",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-17_session.md::section::Cosa è stato fatto",
+ "file_path": ".coding_agent/2026-06-17_session.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "e68d7078a79f85cc",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-17_session.md::section::Paperpal Preflight (prima versione)",
+ "file_path": ".coding_agent/2026-06-17_session.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "35eba4f44ac372a7",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-17_session.md::section::Paperpal Preflight (seconda versione)",
+ "file_path": ".coding_agent/2026-06-17_session.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "23a3830723e0054b",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-17_session.md::section::A5 per Dropbox",
+ "file_path": ".coding_agent/2026-06-17_session.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "42f4752cf872f843",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-17_session.md::section::Stanford review — gap residui",
+ "file_path": ".coding_agent/2026-06-17_session.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "5b7fd34ddf1048ec",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-17_session.md::section::ORCID",
+ "file_path": ".coding_agent/2026-06-17_session.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "3c6f9d4a2b6b033e",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-17_session.md::section::Cover letter",
+ "file_path": ".coding_agent/2026-06-17_session.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "c058ce79b73b2789",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-17_session.md::section::Decisioni prese",
+ "file_path": ".coding_agent/2026-06-17_session.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "228b260ffe7cc289",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-17_session.md::section::Cosa rimane aperto",
+ "file_path": ".coding_agent/2026-06-17_session.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "cd10871882acba44",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-17_session.md::section::Blocchi / dipendenze emerse",
+ "file_path": ".coding_agent/2026-06-17_session.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "7739bf3dd0291e28",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-17_session_B.md::section::Diario sessione 2026-06-17 (B)",
+ "file_path": ".coding_agent/2026-06-17_session_B.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "64a42e56571fcbf4",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-17_session_B.md::section::Cosa è stato fatto",
+ "file_path": ".coding_agent/2026-06-17_session_B.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "86051cba29fec274",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-17_session_B.md::section::Decisioni",
+ "file_path": ".coding_agent/2026-06-17_session_B.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "ae98e8593a00269b",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-17_session_B.md::section::Cosa rimane aperto",
+ "file_path": ".coding_agent/2026-06-17_session_B.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "dd697206235277fd",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": ".coding_agent/2026-06-17_session_B.md::section::Note",
+ "file_path": ".coding_agent/2026-06-17_session_B.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "a55f1547f9bcb8d8",
+ "notes_count": 0
+ },
{
"qualified_name": ".github/dependabot.yml::yaml::version",
"file_path": ".github/dependabot.yml",
@@ -168,7 +440,7 @@
"file_path": ".github/workflows/bioccheck.yaml",
"kind": "yaml_key",
"status": "unread",
- "content_hash": "d4e34afac077d9f7",
+ "content_hash": "9de22700e24fc67f",
"notes_count": 0
},
{
@@ -176,7 +448,7 @@
"file_path": ".github/workflows/bioccheck.yaml",
"kind": "yaml_key",
"status": "unread",
- "content_hash": "b176a87042fcf875",
+ "content_hash": "4742fc4a804ce4f8",
"notes_count": 0
},
{
@@ -619,6 +891,14 @@
"content_hash": "390fddfa4c775b51",
"notes_count": 0
},
+ {
+ "qualified_name": "NEWS.md::section::Changes in version 0.99.6",
+ "file_path": "NEWS.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "816ee97d8de26fe2",
+ "notes_count": 0
+ },
{
"qualified_name": "NEWS.md::section::Changes in version 0.99.5",
"file_path": "NEWS.md",
@@ -795,12 +1075,28 @@
"content_hash": "fcf15295141906f9",
"notes_count": 0
},
+ {
+ "qualified_name": "R/import_CTD.R::.deduplicate_chemicals",
+ "file_path": "R/import_CTD.R",
+ "kind": "function",
+ "status": "unread",
+ "content_hash": "e7f8ec70c6cfe876",
+ "notes_count": 0
+ },
+ {
+ "qualified_name": "R/import_CTD.R::.map_chemical_genes",
+ "file_path": "R/import_CTD.R",
+ "kind": "function",
+ "status": "unread",
+ "content_hash": "aea88a94954b6667",
+ "notes_count": 0
+ },
{
"qualified_name": "R/import_CTD.R::.save_ctd_cache",
"file_path": "R/import_CTD.R",
"kind": "function",
- "status": "read",
- "content_hash": "916d92ff90e97f00",
+ "status": "needs_re_review",
+ "content_hash": "a51395217c003958",
"notes_count": 0
},
{
@@ -816,7 +1112,7 @@
"file_path": "README.md",
"kind": "section",
"status": "unread",
- "content_hash": "5dce6c396d21441a",
+ "content_hash": "26e457c99a9ac541",
"notes_count": 0
},
{
@@ -931,6 +1227,14 @@
"content_hash": "caebd7eac5eaa128",
"notes_count": 0
},
+ {
+ "qualified_name": "README.md::section::End-to-end runnable example",
+ "file_path": "README.md",
+ "kind": "section",
+ "status": "unread",
+ "content_hash": "82ac7f519cae8ca7",
+ "notes_count": 0
+ },
{
"qualified_name": "README.md::section::Input Format",
"file_path": "README.md",
@@ -1168,7 +1472,7 @@
"file_path": "_pkgdown.yml",
"kind": "yaml_key",
"status": "unread",
- "content_hash": "a4bc41f9ca405ee2",
+ "content_hash": "ce620b86aec81060",
"notes_count": 0
},
{
@@ -1179,6 +1483,14 @@
"content_hash": "9f135851e5f600be",
"notes_count": 0
},
+ {
+ "qualified_name": "_pkgdown.yml::yaml::articles[1]",
+ "file_path": "_pkgdown.yml",
+ "kind": "yaml_key",
+ "status": "unread",
+ "content_hash": "413f487fb68a305f",
+ "notes_count": 0
+ },
{
"qualified_name": "_pkgdown.yml::yaml::news",
"file_path": "_pkgdown.yml",
@@ -5292,283 +5604,331 @@
"notes_count": 0
},
{
- "qualified_name": "docs/deps/jquery-3.6.0/jquery-3.6.0.js::jQuery",
- "file_path": "docs/deps/jquery-3.6.0/jquery-3.6.0.js",
+ "qualified_name": "inst/scripts/example_gse311566_full_pipeline.R::log_step",
+ "file_path": "inst/scripts/example_gse311566_full_pipeline.R",
"kind": "function",
"status": "unread",
- "content_hash": "80397a01cc6c1194",
+ "content_hash": "f5045012bac56c62",
"notes_count": 0
},
{
- "qualified_name": "docs/deps/jquery-3.6.0/jquery-3.6.0.js::isArrayLike",
- "file_path": "docs/deps/jquery-3.6.0/jquery-3.6.0.js",
+ "qualified_name": "inst/scripts/example_gse311566_full_pipeline.R::apply_alpha",
+ "file_path": "inst/scripts/example_gse311566_full_pipeline.R",
"kind": "function",
"status": "unread",
- "content_hash": "1efbc8d7223b2bd3",
+ "content_hash": "e8221c442b319843",
"notes_count": 0
},
{
- "qualified_name": "docs/deps/jquery-3.6.0/jquery-3.6.0.js::nodeName",
- "file_path": "docs/deps/jquery-3.6.0/jquery-3.6.0.js",
+ "qualified_name": "inst/scripts/example_gse311566_full_pipeline.R::top_summary",
+ "file_path": "inst/scripts/example_gse311566_full_pipeline.R",
"kind": "function",
"status": "unread",
- "content_hash": "286863c6761ed934",
+ "content_hash": "f992c28aef4ad7e3",
"notes_count": 0
},
{
- "qualified_name": "docs/deps/jquery-3.6.0/jquery-3.6.0.js::camelCase",
- "file_path": "docs/deps/jquery-3.6.0/jquery-3.6.0.js",
+ "qualified_name": "inst/scripts/example_gse311566_full_pipeline.R::rank_in",
+ "file_path": "inst/scripts/example_gse311566_full_pipeline.R",
"kind": "function",
"status": "unread",
- "content_hash": "902db06e4977cd44",
+ "content_hash": "ead363e50888bf1e",
"notes_count": 0
},
{
- "qualified_name": "docs/deps/jquery-3.6.0/jquery-3.6.0.js::expectSync",
- "file_path": "docs/deps/jquery-3.6.0/jquery-3.6.0.js",
- "kind": "function",
+ "qualified_name": "vignettes/ctdR.html::h1::Introduction to ctdR",
+ "file_path": "vignettes/ctdR.html",
+ "kind": "section",
"status": "unread",
- "content_hash": "ae7274b25a1126de",
+ "content_hash": "2a6cc232b97fb927",
"notes_count": 0
},
{
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- "file_path": "docs/deps/jquery-3.6.0/jquery-3.6.0.js",
- "kind": "function",
+ "qualified_name": "vignettes/ctdR.html::h4::2026-06-15",
+ "file_path": "vignettes/ctdR.html",
+ "kind": "section",
"status": "unread",
- "content_hash": "778ae6cb21f8cfec",
+ "content_hash": "cf361a957433198a",
"notes_count": 0
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- "file_path": "docs/deps/jquery-3.6.0/jquery-3.6.0.js",
- "kind": "function",
+ "qualified_name": "vignettes/ctdR.html::h1::Contents",
+ "file_path": "vignettes/ctdR.html",
+ "kind": "section",
"status": "unread",
- "content_hash": "556f8d4bd8bc21fe",
+ "content_hash": "0403ddd4bded18d2",
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- "file_path": "docs/deps/jquery-3.6.0/jquery-3.6.0.min.js",
- "kind": "function",
+ "qualified_name": "vignettes/ctdR.html::h1::1 Overview",
+ "file_path": "vignettes/ctdR.html",
+ "kind": "section",
"status": "unread",
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- "kind": "function",
+ "qualified_name": "vignettes/ctdR.html::h1::2 Data licensing disclaimer",
+ "file_path": "vignettes/ctdR.html",
+ "kind": "section",
"status": "unread",
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+ "qualified_name": "vignettes/ctdR.html::h1::3 Installation",
+ "file_path": "vignettes/ctdR.html",
+ "kind": "section",
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+ "content_hash": "a998c7dd7bc84ab3",
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- "kind": "function",
+ "qualified_name": "vignettes/ctdR.html::h2::3.1 From GitHub (current installation me",
+ "file_path": "vignettes/ctdR.html",
+ "kind": "section",
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+ "content_hash": "f9d7100ebd47ff31",
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- "kind": "function",
+ "qualified_name": "vignettes/ctdR.html::h2::3.2 From Bioconductor (once accepted)",
+ "file_path": "vignettes/ctdR.html",
+ "kind": "section",
"status": "unread",
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"file_path": "docs/deps/jquery-3.6.0/jquery-3.6.0.min.js",
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"status": "unread",
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- "status": "unread",
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+ "qualified_name": "docs/deps/search-1.0.0/fuse.min.js::ue",
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diff --git a/.gitignore b/.gitignore
index 42f0a4d..a8296a4 100644
--- a/.gitignore
+++ b/.gitignore
@@ -11,5 +11,8 @@ ctdR.Rcheck/
# .sestante/ — backlog locale, mai committato
.sestante/
+# .coding_agent/ — diari di sessione AI, mai committati
+.coding_agent/
+
# vignette HTML è artefatto di rmarkdown::render(), non sorgente
vignettes/*.html
diff --git a/NEWS.md b/NEWS.md
index 93abe7a..fe4c72d 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,7 +1,66 @@
# Changes in version 0.99.6
+## New features
+
+* `enrichment_CTD()` gains an `interaction_types` argument: a character
+ vector of CTD `InteractionActions` values (e.g.
+ `"increases^expression"`, `"decreases^expression"`) that filters each
+ chemical's gene set at enrichment time. Gene sets are rebuilt on the
+ fly from the new `ctd_interactions.rda` cache without re-importing;
+ `NULL` (default) retains full backward compatibility. Supported by all
+ four methods (ORA, GSEA, CAMERA, GSVA). Requires `import_CTD()` to be
+ re-run once to generate `ctd_interactions.rda`.
+
+* `enrichment_CTD()` gains a `gene_id_type` argument (`"symbol"` or
+ `"entrez"`) controlling whether the `EnrichedGenes` output column
+ reports HGNC symbols (with Entrez ID fallback for unmapped genes) or
+ raw Entrez IDs. Default `"symbol"` is backward compatible.
+
+* `enrichment_CTD(method = "ORA")` now forwards `universe`, `minGSSize`,
+ and `maxGSSize` to `clusterProfiler::enricher()` via `...`. Setting
+ `universe = de$EntrezID` restricts the background to measured genes,
+ avoiding inflated fold-enrichment estimates. GSEA and GSVA already
+ exposed `minSize`/`maxSize`; CAMERA `...` was already forwarded.
+
+* `import_CTD()` now caches `ctd_interactions.rda`, a long-format table
+ of `(ChemicalID, EntrezID, InteractionActions)` triples used by the
+ new `interaction_types` filter.
+
+* `import_CTD()` reports elapsed time, chemical count, and unique gene
+ count on completion.
+
+* `import_CTD()` detects and warns when the same `ChemicalID` appears
+ with multiple `ChemicalName` values (CTD data quality issue; first
+ name retained). Reports an informational message when the same name
+ is shared by multiple `ChemicalID`s (legitimate parent/derivative
+ pairs).
+
+## Bug fixes
+
+* Fixed `EnrichedGenes` column in GSEA output: was incorrectly set to
+ data frame row indices instead of gene identifiers. Gene labels are
+ now mapped via `AnnotationDbi::mapIds()` in `.run_gsea()`.
+
+* `clusterProfiler::enricher()` messages ("No gene can be mapped",
+ "Expected input gene ID", etc.) are now suppressed via
+ `suppressMessages()`.
+
## Documentation
+* New pkgdown article `vignettes/articles/tutorial_rnaseq_workflow.Rmd`:
+ a complete RNA-seq → chemical enrichment workflow using the full
+ GSE311566 dataset (downloaded from GEO at runtime), `limma` DE, all
+ four methods with recommended parameters, direction-aware GSEA, and a
+ per-method Dexamethasone ranking recap.
+
+* Vignette gains a "Gene set size filters and background universe"
+ section documenting `universe`, `minGSSize`/`maxGSSize` (ORA),
+ `minSize`/`maxSize` (GSEA, GSVA), and CAMERA's implicit minimum of 2
+ genes.
+
+* Added a new `interaction_types` parameter description to the vignette
+ explaining the CTD `verb^noun` vocabulary and direction-aware analysis.
+
* Added a full end-to-end pipeline example at
`inst/scripts/example_gse311566_full_pipeline.R`. The script
downloads the complete GSE311566 Female PBMCs normalised-count
diff --git a/_pkgdown.yml b/_pkgdown.yml
index cf756c2..d33281a 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -6,6 +6,13 @@ template:
primary: "#4575B4"
border-radius: 0.4rem
btn-border-radius: 0.3rem
+ includes:
+ in_header: |
+
+
home:
title: ctdR — Chemical Enrichment Analysis using CTD
diff --git a/vignettes/articles/tutorial_rnaseq_workflow.Rmd b/vignettes/articles/tutorial_rnaseq_workflow.Rmd
index 814548d..87bd6cf 100644
--- a/vignettes/articles/tutorial_rnaseq_workflow.Rmd
+++ b/vignettes/articles/tutorial_rnaseq_workflow.Rmd
@@ -373,8 +373,12 @@ while correcting for inter-gene correlation within the gene set. It is
particularly well suited to expression matrix experiments with a clear
design and contrast.
-We reuse the `design` matrix built for limma. `contrast = 2` selects the
-`groupDex` coefficient (Dex vs DMSO).
+CAMERA does not consume a pre-computed DEG result: it takes the **full
+expression matrix** plus a **`design`** and a **`contrast`**, and
+recomputes the differential signal internally. The chemical→gene "index"
+is built by `ctdR` from CTD targets. We reuse the `design` matrix built
+for limma; here `design` carries the whole layout while `contrast = 2`
+selects *which* coefficient to test — the `groupDex` effect (Dex vs DMSO).
```{r camera}
camera_results <- enrichment_CTD(
diff --git a/vignettes/ctdR.Rmd b/vignettes/ctdR.Rmd
index 610ad47..b452394 100644
--- a/vignettes/ctdR.Rmd
+++ b/vignettes/ctdR.Rmd
@@ -349,9 +349,26 @@ if (is_subset) {
CAMERA tests, for each chemical, whether its target
genes show a stronger differential signal than the rest
-of the transcriptome under a user-supplied design and
-contrast, while correcting for inter-gene correlation
-within the gene set. Reusing the real `expr` / `grp` above:
+of the transcriptome, while correcting for inter-gene
+correlation within the gene set.
+
+Unlike ORA or GSEA, CAMERA does **not** take a pre-computed
+list of differentially expressed genes. Its inputs are the
+**full expression matrix** (`expr`, all genes × all samples)
+together with a **`design`** matrix and a **`contrast`**:
+CAMERA fits the differential model and computes the test
+*internally*. The chemical-to-gene mapping (the gene-set
+"index", built by `ctdR` from CTD targets intersected with
+`rownames(expr)`) is handled for you. Note that `design` and
+`contrast` are two distinct inputs: `design`
+(e.g. `model.matrix(~ grp)`) describes the *whole*
+experimental layout — intercept plus any covariates — while
+`contrast` selects *which* coefficient to test (here column 2,
+Dex vs DMSO). This separation lets you adjust for batch or
+other nuisance covariates while keeping the test focused on a
+single comparison.
+
+Reusing the real `expr` / `grp` above:
```{r camera}
design <- model.matrix(~ grp)