agent-skill-manager 1.22.0 → 2.1.0

package/README.md

@@ -275,7 +275,7 @@ asm publish --yes ./my-skill
 4. Test with your AI agent
 5. **Security audit** — `asm audit security awesome-skill`
 6. **Verify metadata** — `asm inspect awesome-skill`
-7. **Score quality** — `asm eval ./awesome-skill` (add `--runtime` for skillgrade runtime evals)
+7. **Score quality** — `asm eval ./awesome-skill`
 8. Push to GitHub
 9. **Verify install flow** — `asm install github:you/awesome-skill`
 10. **Publish to registry** — `asm publish ./awesome-skill`
@@ -318,36 +318,25 @@ asm index search "your-skill" --json
 
 Each indexed skill in the output JSON includes `"verified": true` or `"verified": false`. If verification fails, the ingestion debug log (set `ASM_DEBUG=1`) prints the specific reasons.
 
-### Runtime Evaluation (`asm eval`)
+### Quality Evaluation (`asm eval`)
 
-Static verification tells you the SKILL.md is well-formed. `asm eval` goes further and answers two orthogonal questions about any skill on disk:
-
-1. **Is it well-written?** — `quality@1.0.0` ships by default and runs a scored rubric over structure, frontmatter, clarity, and safety.
-2. **Does it actually work?** — `asm eval --runtime` shells out to [skillgrade](https://github.com/mgechev/skillgrade) for deterministic + LLM-judge runtime evals in a Docker sandbox, with CI-ready exit codes.
-
-**Zero-setup install:** skillgrade ships as a direct dependency of `asm`. After `npm install -g agent-skill-manager`, `asm eval --runtime` just works — no `npm i -g skillgrade`, no PATH hijacking. Override with `ASM_SKILLGRADE_BIN=/path/to/skillgrade` if you want to point at a different binary.
+Static verification tells you the SKILL.md is well-formed. `asm eval` goes further: the built-in `quality` provider runs a scored rubric over structure, frontmatter, clarity, prompt engineering, context efficiency, safety, testability, and naming — and emits per-category scores plus concrete suggestions for improvement. Zero setup, zero API keys, zero external binaries.
 
 ```bash
-# Static quality lint (default)
+# Score the skill and print recommendations
 asm eval ./my-skill
 
-# Scaffold eval.yaml for runtime tests
-asm eval ./my-skill --runtime init
+# CI-friendly machine-readable output
+asm eval ./my-skill --machine
 
-# Run the skillgrade runtime provider
-asm eval ./my-skill --runtime --preset smoke
-
-# CI-friendly JSON
-asm eval ./my-skill --runtime --machine --threshold 0.8
+# Apply deterministic auto-fixes to SKILL.md
+asm eval ./my-skill --fix
 
 # List registered eval providers
 asm eval-providers list
-
-# Diff two provider versions before promoting an upgrade
-asm eval ./my-skill --compare skillgrade@1.0.0,skillgrade@2.0.0-next
 ```
 
-The eval surface is a pluggable provider framework: each provider implements a common `EvalProvider` contract and resolves via semver range, so you can pin a version in `~/.asm/config.yml`, diff two versions side-by-side with `--compare`, and add new providers without touching the CLI. See [`docs/eval-providers.md`](./docs/eval-providers.md) for the provider model and [`docs/skillgrade-integration.md`](./docs/skillgrade-integration.md) for skillgrade install, presets, and CI usage.
+The eval surface is a pluggable provider framework: each provider implements a common `EvalProvider` contract and resolves via semver range. See [`docs/eval-providers.md`](./docs/eval-providers.md) for the provider model.
 
 ---
 
@@ -536,7 +525,7 @@ Need a tool not listed? Add a custom provider entry to the config.
 Yes. `asm` is MIT licensed and free forever. No accounts, no telemetry, no paywalls.
 
 **Is it actively maintained?**
-v1.22.0 shipped on April 19, 2026. The project has had 31 releases. Check the [changelog](docs/CHANGELOG.md) for the full history.
+v2.1.0 shipped on April 20, 2026. The project has had 33 releases. Check the [changelog](docs/CHANGELOG.md) for the full history.
 
 **Which AI agents does it support?**
 18 providers built-in: Claude Code, Codex, OpenClaw, Cursor, Windsurf, Cline, Roo Code, Continue, GitHub Copilot, Aider, OpenCode, Zed, Augment, Amp, Gemini CLI, Google Antigravity, Hermes, and a generic Agents provider. All 18 are enabled by default; disable any you don't need via `asm config edit`. You can also add any custom agent that stores skills as directories with a `SKILL.md` file.
@@ -600,8 +589,7 @@ asm
 | `asm link <path> [<path2> ...]` | Symlink one or more local skills for live development |
 | `asm audit`                     | Detect duplicate skills                               |
 | `asm audit security <name>`     | Run security audit on a skill                         |
-| `asm eval <skill>`              | Score a skill via the pluggable eval framework        |
-| `asm eval <skill> --runtime`    | Runtime evaluation via skillgrade (LLM-judge)         |
+| `asm eval <skill>`              | Score a skill and print improvement suggestions       |
 | `asm eval-providers list`       | List registered eval providers and versions           |
 | `asm stats`                     | Show aggregate skill metrics dashboard                |
 | `asm export`                    | Export skill inventory as JSON manifest               |
@@ -670,12 +658,6 @@ Score a skill with the static quality provider:
 asm eval ./my-skill
 ```
 
-Run the skillgrade runtime evaluator (requires `skillgrade` on PATH):
-
-```bash
-asm eval ./my-skill --runtime --preset smoke
-```
-
 List registered eval providers:
 
 ```bash
@@ -816,7 +798,7 @@ asm install github:user/my-skill -p claude --yes --json
 | `-y, --yes`              | Skip confirmation prompt                                   |
 | `--json`                 | Output result as JSON                                      |
 
-**Multi-skill repo support:** When a repo doesn't have `SKILL.md` at the root, `asm` automatically scans for skills in subdirectories (up to 3 levels deep). In interactive mode, it presents a numbered picker. Use `--path` to target a specific skill or `--all` to batch-install everything.
+**Multi-skill repo support:** When a repo doesn't have `SKILL.md` at the root, `asm` automatically scans for skills in subdirectories (up to 5 levels deep). In interactive mode, it presents a numbered picker. Use `--path` to target a specific skill or `--all` to batch-install everything.
 
 The install command clones the repository, validates `SKILL.md` files, scans for security warnings, previews skill metadata, and installs to the selected provider's global skill directory. Requires `git` on PATH.
 
@@ -1161,18 +1143,17 @@ agent-skill-manager/
 <details>
 <summary><strong>Documentation</strong></summary>
 
-| Document                                                 | Description                                              |
-| -------------------------------------------------------- | -------------------------------------------------------- |
-| [Architecture](docs/ARCHITECTURE.md)                     | System design, components, and data flow                 |
-| [Eval Providers](docs/eval-providers.md)                 | Pluggable eval framework, `--compare`, adding a provider |
-| [Skillgrade Integration](docs/skillgrade-integration.md) | Install, presets, CI usage, troubleshooting              |
-| [Development](docs/DEVELOPMENT.md)                       | Local setup, testing, and debugging                      |
-| [Deployment](docs/DEPLOYMENT.md)                         | Publishing and CI pipeline                               |
-| [Changelog](docs/CHANGELOG.md)                           | Version history                                          |
-| [Brand Kit](docs/brand_kit.md)                           | Logo, colors, and typography                             |
-| [Contributing](CONTRIBUTING.md)                          | How to contribute                                        |
-| [Security](SECURITY.md)                                  | Vulnerability reporting                                  |
-| [Code of Conduct](CODE_OF_CONDUCT.md)                    | Community guidelines                                     |
+| Document                                 | Description                                        |
+| ---------------------------------------- | -------------------------------------------------- |
+| [Architecture](docs/ARCHITECTURE.md)     | System design, components, and data flow           |
+| [Eval Providers](docs/eval-providers.md) | Pluggable eval framework and how to add a provider |
+| [Development](docs/DEVELOPMENT.md)       | Local setup, testing, and debugging                |
+| [Deployment](docs/DEPLOYMENT.md)         | Publishing and CI pipeline                         |
+| [Changelog](docs/CHANGELOG.md)           | Version history                                    |
+| [Brand Kit](docs/brand_kit.md)           | Logo, colors, and typography                       |
+| [Contributing](CONTRIBUTING.md)          | How to contribute                                  |
+| [Security](SECURITY.md)                  | Vulnerability reporting                            |
+| [Code of Conduct](CODE_OF_CONDUCT.md)    | Community guidelines                               |
 
 </details>
 

package/data/skill-index/Affitor_affiliate-skills.json

@@ -2,8 +2,8 @@
   "repoUrl": "https://github.com/Affitor/affiliate-skills.git",
   "owner": "Affitor",
   "repo": "affiliate-skills",
-  "updatedAt": "2026-03-27T23:21:27.196Z",
-  "skillCount": 48,
+  "updatedAt": "2026-04-20T06:33:11.236Z",
+  "skillCount": 53,
   "skills": [
     {
       "name": "ab-test-generator",
@@ -125,6 +125,18 @@
       "relPath": "skills/meta/compliance-checker",
       "verified": true
     },
+    {
+      "name": "content-angle-ranker",
+      "description": "Rank content angles by engagement data, competition level, and platform fit. Data-driven angle selection instead of guesswork. Use this skill when the user has a keyword or product and needs to decide WHAT to create, which angle to take, which format to use, or which platform to target. Triggers on: \"what angle should I use\", \"rank content ideas for [keyword]\", \"best angle for [product]\", \"which content idea will perform best\", \"help me pick an angle\", \"what should I write about\", \"content angle for [topic]\", \"rank my content ideas\", \"which approach will get the most views\", \"data-driven content planning\", \"angle ranker\", \"content scoring\", \"which hook should I use\", \"compare these content ideas\", \"prioritize my content angles\", \"what video should I make\".",
+      "version": "1.0",
+      "license": "MIT",
+      "creator": "",
+      "compatibility": "Claude Code, ChatGPT, Gemini CLI, Cursor, Windsurf, OpenClaw, any AI agent",
+      "allowedTools": [],
+      "installUrl": "github:Affitor/affiliate-skills:skills/research/content-angle-ranker",
+      "relPath": "skills/research/content-angle-ranker",
+      "verified": true
+    },
     {
       "name": "content-decay-detector",
       "description": "Monitor existing content for ranking drops and trigger refresh workflows. Triggers on: \"check for content decay\", \"which content needs updating\", \"content refresh\", \"ranking drops\", \"traffic decline\", \"stale content\", \"content audit\", \"what to refresh\", \"outdated content\", \"content performance check\", \"update old articles\", \"declining rankings\", \"content maintenance\", \"refresh priority list\", \"which articles are losing traffic\", \"SEO content audit\".",
@@ -173,6 +185,18 @@
       "relPath": "skills/automation/content-repurposer",
       "verified": true
     },
+    {
+      "name": "content-research-brief",
+      "description": "Research trending topics, collect source articles, and generate a structured research brief for content creation. Stop writing from thin air — write from real sources. Use this skill when the user wants to research a topic before writing, collect sources for an article, create a research-backed content brief, or says \"research [topic] for me\", \"find sources about [keyword]\", \"content brief for [topic]\", \"what's the latest on [product]\", \"research before writing\", \"collect articles about [keyword]\", \"trending news about [topic]\", \"gather sources for my article\", \"brief me on [topic]\", \"what are people saying about [product]\", \"news roundup for [keyword]\", \"research brief\", \"source collection\", \"content research\", \"prep research for writing\".",
+      "version": "1.0",
+      "license": "MIT",
+      "creator": "",
+      "compatibility": "Claude Code, ChatGPT, Gemini CLI, Cursor, Windsurf, OpenClaw, any AI agent",
+      "allowedTools": [],
+      "installUrl": "github:Affitor/affiliate-skills:skills/content/content-research-brief",
+      "relPath": "skills/content/content-research-brief",
+      "verified": true
+    },
     {
       "name": "conversion-tracker",
       "description": "Set up affiliate conversion tracking with UTM parameters and link tagging. Triggers on: \"set up tracking\", \"create UTM links\", \"track my affiliate links\", \"tracking pixels\", \"click attribution\", \"organize my links\", \"UTM parameters\", \"tag my links\", \"campaign tracking\", \"link tracking setup\", \"prepare for launch\", \"debug attribution\", \"tracking spreadsheet\".",
@@ -269,6 +293,18 @@
       "relPath": "skills/blog/how-to-tutorial-writer",
       "verified": true
     },
+    {
+      "name": "infographic-generator",
+      "description": "Generate branded infographic specifications from any content or data. Outputs structured layout, copy, data visualization, and color scheme — ready to render as HTML/CSS, Satori, Canva, or any design tool. Use this skill when the user wants an infographic, data visual, social media image, comparison chart, stat card, or says \"create an infographic for [content]\", \"make a visual for my LinkedIn post\", \"design an image for [topic]\", \"stat graphic for [data]\", \"comparison infographic\", \"branded image\", \"social media graphic\", \"infographic for [blog post]\", \"data visualization\", \"visual content\", \"image for my post\", \"LinkedIn carousel image\", \"feature comparison chart\", \"pricing table image\".",
+      "version": "1.0",
+      "license": "MIT",
+      "creator": "",
+      "compatibility": "Claude Code, ChatGPT, Gemini CLI, Cursor, Windsurf, OpenClaw, any AI agent",
+      "allowedTools": [],
+      "installUrl": "github:Affitor/affiliate-skills:skills/content/infographic-generator",
+      "relPath": "skills/content/infographic-generator",
+      "verified": true
+    },
     {
       "name": "internal-linking-optimizer",
       "description": "Analyze site's internal link structure and optimize for hub-and-spoke SEO architecture. Triggers on: \"optimize internal links\", \"internal linking\", \"link structure\", \"hub and spoke links\", \"orphan pages\", \"link equity\", \"internal link audit\", \"fix my internal links\", \"link architecture\", \"site structure optimization\", \"internal linking strategy\", \"link flow\", \"improve site structure\", \"find orphan pages\", \"maximize link equity\", \"internal link map\".",
@@ -521,6 +557,30 @@
       "relPath": "skills/content/tiktok-script-writer",
       "verified": true
     },
+    {
+      "name": "traffic-analyzer",
+      "description": "Analyze website traffic, global rank, engagement metrics, and traffic sources for any domain. Use this skill to evaluate affiliate program websites, compare competitor traffic, assess advertiser strength, or understand where an audience comes from. Triggers on: \"analyze traffic for [domain]\", \"how much traffic does [site] get\", \"compare traffic between [site A] and [site B]\", \"is [program] worth promoting based on traffic\", \"traffic analysis\", \"website analytics for [domain]\", \"where does [site] get traffic\", \"check if [advertiser] is legit\", \"evaluate [program] website health\", \"SimilarWeb analysis\", \"traffic sources for [domain]\", \"how popular is [site]\", \"website rank\", \"domain authority check\", \"compare affiliate program websites\".",
+      "version": "1.0",
+      "license": "MIT",
+      "creator": "",
+      "compatibility": "Claude Code, ChatGPT, Gemini CLI, Cursor, Windsurf, OpenClaw, any AI agent",
+      "allowedTools": [],
+      "installUrl": "github:Affitor/affiliate-skills:skills/research/traffic-analyzer",
+      "relPath": "skills/research/traffic-analyzer",
+      "verified": true
+    },
+    {
+      "name": "trending-content-scout",
+      "description": "Scan social platforms for top-performing content by engagement before you create anything. Use this skill when the user wants to see what content is winning in a niche, find viral content patterns, research what's working on YouTube/TikTok/X/Reddit, benchmark engagement, discover content gaps, or says \"what content is working for [topic]\", \"show me top performing content about [keyword]\", \"what's trending in [niche]\", \"find viral content about [product]\", \"content research for [keyword]\", \"what gets views in [niche]\", \"engagement analysis for [topic]\", \"scout the competition\", \"what videos are getting the most views about [keyword]\", \"social listening for [topic]\", \"trending content in [niche]\", \"top content analysis\", \"what hooks work for [keyword]\", \"content intelligence\", \"find winning formats\".",
+      "version": "1.0",
+      "license": "MIT",
+      "creator": "",
+      "compatibility": "Claude Code, ChatGPT, Gemini CLI, Cursor, Windsurf, OpenClaw, any AI agent",
+      "allowedTools": [],
+      "installUrl": "github:Affitor/affiliate-skills:skills/research/trending-content-scout",
+      "relPath": "skills/research/trending-content-scout",
+      "verified": true
+    },
     {
       "name": "twitter-thread-writer",
       "description": "Write X/Twitter threads that get bookmarked, shared, and drive affiliate clicks. Use this skill when the user asks about writing Twitter threads, X threads, tweet threads for affiliate marketing, or says \"write a thread about X\", \"Twitter thread promoting X\", \"X thread for affiliate\", \"write tweets that go viral\", \"thread that sells without selling\", \"educational thread with affiliate CTA\", \"Twitter content for affiliate marketing\", \"how to promote X on Twitter\", \"write a thread my audience will bookmark\", \"tweet storm about affiliate product\".",

package/data/skill-index/Eronred_aso-skills.json

@@ -2,7 +2,7 @@
   "repoUrl": "https://github.com/Eronred/aso-skills.git",
   "owner": "Eronred",
   "repo": "aso-skills",
-  "updatedAt": "2026-03-27T23:21:30.962Z",
+  "updatedAt": "2026-04-20T06:33:17.305Z",
   "skillCount": 30,
   "skills": [
     {

package/data/skill-index/GPTomics_bioSkills.json

@@ -2,8 +2,8 @@
   "repoUrl": "https://github.com/GPTomics/bioSkills.git",
   "owner": "GPTomics",
   "repo": "bioSkills",
-  "updatedAt": "2026-03-27T23:21:36.781Z",
-  "skillCount": 426,
+  "updatedAt": "2026-04-20T06:33:29.401Z",
+  "skillCount": 439,
   "skills": [
     {
       "name": "bio-admet-prediction",
@@ -89,6 +89,18 @@
       "relPath": "alignment/msa-statistics",
       "verified": true
     },
+    {
+      "name": "bio-alignment-multiple",
+      "description": "Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm selection based on dataset size, sequence divergence, and downstream application. Use when aligning three or more homologous sequences for phylogenetics, conservation analysis, or evolutionary studies.",
+      "version": "0.0.0",
+      "license": "",
+      "creator": "",
+      "compatibility": "",
+      "allowedTools": [],
+      "installUrl": "github:GPTomics/bioSkills:alignment/multiple-alignment",
+      "relPath": "alignment/multiple-alignment",
+      "verified": true
+    },
     {
       "name": "bio-alignment-pairwise",
       "description": "Perform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner. Use when comparing two sequences, finding optimal alignments, scoring similarity, and identifying local or global matches between DNA, RNA, or protein sequences.",
@@ -331,7 +343,7 @@
     },
     {
       "name": "bio-chipseq-differential-binding",
-      "description": "Differential binding analysis using DiffBind. Compare ChIP-seq peaks between conditions with statistical rigor. Requires replicate samples. Outputs differentially bound regions with fold changes and p-values. Use when comparing ChIP-seq binding between conditions.",
+      "description": "Identifies differentially bound ChIP-seq regions between conditions using DiffBind (from BAMs), DESeq2, or PyDESeq2 (from count matrices). Handles normalization, statistical testing, and fold-change estimation with ChIP-seq-specific considerations. Use when comparing ChIP-seq binding between experimental conditions.",
       "version": "0.0.0",
       "license": "",
       "creator": "",
@@ -355,7 +367,7 @@
     },
     {
       "name": "bio-chipseq-peak-annotation",
-      "description": "Annotate ChIP-seq peaks to genomic features and genes using ChIPseeker. Assign peaks to promoters, exons, introns, and intergenic regions. Find nearest genes and calculate distance to TSS. Generate annotation plots and statistics. Use when annotating ChIP-seq peaks to genomic features.",
+      "description": "Annotate ChIP-seq peaks to genomic features and nearest genes. Classify peaks as promoter, exon, intron, or intergenic using ChIPseeker (R), HOMER annotatePeaks.pl (CLI), or Python (pandas/pyranges). Supports pre-built annotation databases and custom GTF files. Handles promoter definition, feature priority, category collapsing, and signed distance-to-TSS. Use when assigning genomic context to ChIP-seq peaks or linking peaks to target genes.",
       "version": "0.0.0",
       "license": "",
       "creator": "",
@@ -367,7 +379,7 @@
     },
     {
       "name": "bio-chipseq-peak-calling",
-      "description": "ChIP-seq peak calling using MACS3 (or MACS2). Call narrow peaks for transcription factors or broad peaks for histone modifications. Supports input control, fragment size modeling, and various output formats including narrowPeak and broadPeak BED files. Use when calling peaks from ChIP-seq alignments.",
+      "description": "ChIP-seq peak calling using MACS3 and HOMER findPeaks. Call narrow peaks for transcription factors or broad peaks for histone modifications. Supports single-caller and multi-caller consensus approaches, input control, fragment size modeling, and various output formats. Use when calling peaks from ChIP-seq alignments.",
       "version": "0.0.0",
       "license": "",
       "creator": "",
@@ -413,6 +425,78 @@
       "relPath": "chip-seq/chipseq-visualization",
       "verified": true
     },
+    {
+      "name": "bio-clinical-biostatistics-categorical-tests",
+      "description": "Tests associations between categorical variables in clinical data using chi-square, Fisher's exact, and Cochran-Mantel-Haenszel tests. Computes effect sizes and post-hoc pairwise comparisons. Use when analyzing categorical outcomes or testing treatment-outcome independence in clinical trials.",
+      "version": "0.0.0",
+      "license": "",
+      "creator": "",
+      "compatibility": "",
+      "allowedTools": [],
+      "installUrl": "github:GPTomics/bioSkills:clinical-biostatistics/categorical-tests",
+      "relPath": "clinical-biostatistics/categorical-tests",
+      "verified": true
+    },
+    {
+      "name": "bio-clinical-biostatistics-cdisc-data",
+      "description": "Reads and prepares CDISC SDTM clinical trial data for analysis. Handles domain tables (DM, AE, EX, VS, LB), USUBJID-based joins, event-to-subject aggregation, and SUPPQUAL pivoting. Use when working with clinical trial datasets in CDISC/SDTM format or .xpt files.",
+      "version": "0.0.0",
+      "license": "",
+      "creator": "",
+      "compatibility": "",
+      "allowedTools": [],
+      "installUrl": "github:GPTomics/bioSkills:clinical-biostatistics/cdisc-data-handling",
+      "relPath": "clinical-biostatistics/cdisc-data-handling",
+      "verified": true
+    },
+    {
+      "name": "bio-clinical-biostatistics-effect-measures",
+      "description": "Computes and interprets treatment effect measures including odds ratios, risk ratios, number needed to treat, and confidence intervals from clinical trial data. Covers crude and adjusted measures, non-collapsibility of odds ratios, and forest plot visualization. Use when reporting treatment effects or comparing effect sizes across clinical studies.",
+      "version": "0.0.0",
+      "license": "",
+      "creator": "",
+      "compatibility": "",
+      "allowedTools": [],
+      "installUrl": "github:GPTomics/bioSkills:clinical-biostatistics/effect-measures",
+      "relPath": "clinical-biostatistics/effect-measures",
+      "verified": true
+    },
+    {
+      "name": "bio-clinical-biostatistics-logistic-regression",
+      "description": "Performs logistic regression for clinical trial outcomes including binary, ordinal, and multinomial models. Extracts odds ratios with confidence intervals, handles covariate adjustment, and provides Firth penalized regression for rare events or separation. Use when modeling binary or ordinal endpoints from clinical data.",
+      "version": "0.0.0",
+      "license": "",
+      "creator": "",
+      "compatibility": "",
+      "allowedTools": [],
+      "installUrl": "github:GPTomics/bioSkills:clinical-biostatistics/logistic-regression",
+      "relPath": "clinical-biostatistics/logistic-regression",
+      "verified": true
+    },
+    {
+      "name": "bio-clinical-biostatistics-subgroup-analysis",
+      "description": "Performs stratified and subgroup analyses for clinical trial data. Covers Mantel-Haenszel pooling, Breslow-Day homogeneity testing, interaction terms in regression, multiple comparisons correction, and forest plot visualization. Use when analyzing treatment effects across patient subgroups or controlling for stratification variables.",
+      "version": "0.0.0",
+      "license": "",
+      "creator": "",
+      "compatibility": "",
+      "allowedTools": [],
+      "installUrl": "github:GPTomics/bioSkills:clinical-biostatistics/subgroup-analysis",
+      "relPath": "clinical-biostatistics/subgroup-analysis",
+      "verified": true
+    },
+    {
+      "name": "bio-clinical-biostatistics-trial-reporting",
+      "description": "Prepares statistical tables and reports for clinical trials following regulatory standards. Generates Table 1 baseline characteristics, defines analysis populations (ITT, per-protocol, safety), performs multiple imputation for missing data, and follows CONSORT and ICH E9 guidelines. Use when creating analysis reports, handling missing data, or preparing regulatory submissions from clinical trials.",
+      "version": "0.0.0",
+      "license": "",
+      "creator": "",
+      "compatibility": "",
+      "allowedTools": [],
+      "installUrl": "github:GPTomics/bioSkills:clinical-biostatistics/trial-reporting",
+      "relPath": "clinical-biostatistics/trial-reporting",
+      "verified": true
+    },
     {
       "name": "bio-clinical-databases-clinvar-lookup",
       "description": "Query ClinVar for variant pathogenicity classifications, review status, and disease associations via REST API or local VCF. Use when determining clinical significance of variants for diagnostic or research purposes.",
@@ -1397,6 +1481,18 @@
       "relPath": "expression-matrix/metadata-joins",
       "verified": true
     },
+    {
+      "name": "bio-expression-matrix-normalization",
+      "description": "Normalize and transform RNA-seq count matrices for differential expression, visualization, and clustering. Covers between-sample (TMM, RLE, upper quartile), within-sample (TPM, FPKM), variance-stabilizing (VST, rlog), and single-cell (scran) methods. Use when choosing or applying normalization to expression data.",
+      "version": "0.0.0",
+      "license": "",
+      "creator": "",
+      "compatibility": "",
+      "allowedTools": [],
+      "installUrl": "github:GPTomics/bioSkills:expression-matrix/normalization",
+      "relPath": "expression-matrix/normalization",
+      "verified": true
+    },
     {
       "name": "bio-expression-matrix-sparse-handling",
       "description": "Work with sparse matrices for memory-efficient storage of count data. Use when dealing with single-cell data or large bulk RNA-seq datasets where most values are zero.",
@@ -2443,7 +2539,7 @@
     },
     {
       "name": "bio-metabolomics-statistical-analysis",
-      "description": "Statistical analysis for metabolomics data. Covers univariate testing, multivariate methods (PCA, PLS-DA), and biomarker discovery. Use when identifying differentially abundant metabolites or building classification models.",
+      "description": "Statistical analysis for metabolomics data. Covers preprocessing (log2 transformation, normalization), limma moderated testing with empirical Bayes, Welch's t-tests with BH correction, fold change estimation, and multivariate methods (PCA, PLS-DA, OPLS-DA). Use when identifying differentially abundant metabolites or building classification models.",
       "version": "0.0.0",
       "license": "",
       "creator": "",
@@ -2597,6 +2693,18 @@
       "relPath": "methylation-analysis/methylation-calling",
       "verified": true
     },
+    {
+      "name": "bio-methylation-differential-cpg",
+      "description": "Per-CpG differential methylation testing from bisulfite sequencing count data or beta-value matrices. Covers beta and M-value computation, coverage filtering, statistical tests (Welch t-test, Mann-Whitney, limma, DSS beta-binomial), multiple testing correction, and effect size calculation. Use when comparing methylation at individual CpG sites between experimental groups from WGBS, RRBS, or targeted bisulfite sequencing.",
+      "version": "0.0.0",
+      "license": "",
+      "creator": "",
+      "compatibility": "",
+      "allowedTools": [],
+      "installUrl": "github:GPTomics/bioSkills:methylation-analysis/differential-cpg-testing",
+      "relPath": "methylation-analysis/differential-cpg-testing",
+      "verified": true
+    },
     {
       "name": "bio-methylation-dmr-detection",
       "description": "Differentially methylated region (DMR) detection using methylKit tiles, bsseq BSmooth, and DMRcate. Use when identifying contiguous genomic regions with methylation differences between experimental conditions or cell types.",
@@ -2957,9 +3065,21 @@
       "relPath": "phasing-imputation/reference-panels",
       "verified": true
     },
+    {
+      "name": "bio-phylo-bayesian-inference",
+      "description": "Run Bayesian phylogenetic analysis with MrBayes, BEAST2, RevBayes, and PhyloBayes including MCMC convergence diagnostics and model comparison. Use when needing posterior probability support, Bayesian model averaging, site-heterogeneous models for deep phylogenies, or formal model comparison via stepping-stone sampling.",
+      "version": "0.0.0",
+      "license": "",
+      "creator": "",
+      "compatibility": "",
+      "allowedTools": [],
+      "installUrl": "github:GPTomics/bioSkills:phylogenetics/bayesian-inference",
+      "relPath": "phylogenetics/bayesian-inference",
+      "verified": true
+    },
     {
       "name": "bio-phylo-distance-calculations",
-      "description": "Compute evolutionary distances and build phylogenetic trees using Biopython Bio.Phylo.TreeConstruction. Use when creating distance matrices from alignments, building NJ/UPGMA trees, or generating bootstrap consensus trees.",
+      "description": "Compute evolutionary distances and build phylogenetic trees using Biopython Bio.Phylo.TreeConstruction. Use when creating distance matrices from alignments, building NJ/UPGMA trees, generating bootstrap consensus, or needing quick exploratory phylogenies before running full ML analysis.",
       "version": "0.0.0",
       "license": "",
       "creator": "",
@@ -2969,9 +3089,21 @@
       "relPath": "phylogenetics/distance-calculations",
       "verified": true
     },
+    {
+      "name": "bio-phylo-divergence-dating",
+      "description": "Estimate divergence times using molecular clock models with BEAST2, MCMCTree, and TreePL. Use when dating speciation events, calibrating phylogenies with fossils, choosing between strict and relaxed clock models, or estimating evolutionary rates across lineages.",
+      "version": "0.0.0",
+      "license": "",
+      "creator": "",
+      "compatibility": "",
+      "allowedTools": [],
+      "installUrl": "github:GPTomics/bioSkills:phylogenetics/divergence-dating",
+      "relPath": "phylogenetics/divergence-dating",
+      "verified": true
+    },
     {
       "name": "bio-phylo-modern-tree-inference",
-      "description": "Build maximum likelihood phylogenetic trees using IQ-TREE2 and RAxML-ng. Use when inferring publication-quality trees with model selection, ultrafast bootstrap, or partitioned analyses from sequence alignments.",
+      "description": "Build maximum likelihood phylogenetic trees using IQ-TREE2 and RAxML-NG with expert model selection, branch support assessment, and topology testing. Use when inferring publication-quality ML trees, selecting substitution models, interpreting bootstrap and concordance factor support, or running partitioned phylogenomic analyses.",
       "version": "0.0.0",
       "license": "",
       "creator": "",
@@ -2981,6 +3113,18 @@
       "relPath": "phylogenetics/modern-tree-inference",
       "verified": true
     },
+    {
+      "name": "bio-phylo-species-trees",
+      "description": "Estimate species trees using coalescent methods including ASTRAL-III, wASTRAL, ASTRAL-Pro, SVDQuartets, and BPP. Use when multi-locus data shows gene tree discordance from incomplete lineage sorting, when in the anomaly zone where concatenation is misleading, or when computing concordance factors to assess topological support.",
+      "version": "0.0.0",
+      "license": "",
+      "creator": "",
+      "compatibility": "",
+      "allowedTools": [],
+      "installUrl": "github:GPTomics/bioSkills:phylogenetics/species-trees",
+      "relPath": "phylogenetics/species-trees",
+      "verified": true
+    },
     {
       "name": "bio-phylo-tree-io",
       "description": "Read, write, and convert phylogenetic tree files using Biopython Bio.Phylo. Use when parsing Newick, Nexus, PhyloXML, or NeXML tree formats, converting between formats, or handling multiple trees.",
@@ -2995,7 +3139,7 @@
     },
     {
       "name": "bio-phylo-tree-manipulation",
-      "description": "Modify phylogenetic tree structure using Biopython Bio.Phylo. Use when rooting trees with outgroups or midpoint, pruning taxa, collapsing clades, ladderizing branches, or extracting subtrees.",
+      "description": "Modify phylogenetic tree structure using Biopython Bio.Phylo. Use when rooting trees with outgroups, midpoint, or MAD methods, pruning taxa, collapsing clades, ladderizing branches, or extracting subtrees. Includes rooting method decision guidance.",
       "version": "0.0.0",
       "license": "",
       "creator": "",
@@ -3007,7 +3151,7 @@
     },
     {
       "name": "bio-phylo-tree-visualization",
-      "description": "Draw and export phylogenetic trees using Biopython Bio.Phylo with matplotlib. Use when creating publication-quality tree figures, customizing colors and labels, or exporting to image formats.",
+      "description": "Draw and export phylogenetic trees using Biopython Bio.Phylo with matplotlib and modern alternatives. Use when creating tree figures, customizing colors and labels, exporting to image formats, or choosing between Bio.Phylo, ggtree, ETE4, and iTOL for publication.",
       "version": "0.0.0",
       "license": "",
       "creator": "",
@@ -3163,7 +3307,7 @@
     },
     {
       "name": "bio-proteomics-differential-abundance",
-      "description": "Statistical testing for differentially abundant proteins between conditions. Covers limma and MSstats workflows with multiple testing correction. Use when identifying proteins with significant abundance changes between experimental groups.",
+      "description": "Statistical testing for differentially abundant proteins between conditions. Covers preprocessing (log2 transformation, normalization), limma and DEqMS workflows with empirical Bayes moderation, fold change shrinkage for accurate effect size estimation, and Python alternatives. Use when identifying proteins with significant abundance changes between experimental groups.",
       "version": "0.0.0",
       "license": "",
       "creator": "",
@@ -4447,7 +4591,7 @@
     },
     {
       "name": "bio-variant-annotation",
-      "description": "Comprehensive variant annotation using bcftools annotate/csq, VEP, SnpEff, and ANNOVAR. Add database annotations, predict functional consequences, and assess clinical significance. Use when annotating variants with functional and clinical information.",
+      "description": "Comprehensive variant annotation using bcftools annotate/csq, VEP, SnpEff, and ANNOVAR. Add database annotations, predict functional consequences, and assess clinical significance with MANE transcript selection and pathogenicity scoring. Use when annotating variants with functional and clinical information.",
       "version": "0.0.0",
       "license": "",
       "creator": "",
@@ -4483,7 +4627,7 @@
     },
     {
       "name": "bio-variant-calling-deepvariant",
-      "description": "Deep learning-based variant calling with Google DeepVariant. Provides high accuracy for germline SNPs and indels from Illumina, PacBio, and ONT data. Use when calling variants with DeepVariant deep learning caller.",
+      "description": "Deep learning-based variant calling with Google DeepVariant. Provides high accuracy for germline SNPs and indels from Illumina, PacBio, and ONT data. Use when calling variants with DeepVariant deep learning caller or when highest germline calling accuracy is required.",
       "version": "0.0.0",
       "license": "",
       "creator": "",
@@ -4519,7 +4663,7 @@
     },
     {
       "name": "bio-variant-calling-structural-variant-calling",
-      "description": "Call structural variants (SVs) from short-read sequencing using Manta, Delly, and LUMPY. Detects deletions, insertions, inversions, duplications, and translocations that are too large for standard SNV callers. Use when detecting structural variants from short-read data.",
+      "description": "Call structural variants (SVs) from sequencing data using Manta, Delly, GRIDSS, and LUMPY. Detects deletions, insertions, inversions, duplications, and translocations too large for standard SNV callers. Use when detecting structural variants from short-read or long-read data and building consensus callsets.",
       "version": "0.0.0",
       "license": "",
       "creator": "",
@@ -4531,7 +4675,7 @@
     },
     {
       "name": "bio-variant-normalization",
-      "description": "Normalize indel representation and split multiallelic variants using bcftools norm. Use when comparing variants from different callers or preparing VCF for downstream analysis.",
+      "description": "Normalize indel representation, decompose MNPs, and split multiallelic variants using bcftools norm. Use when comparing variants from different callers, preparing VCF for database annotation, or merging VCFs from multiple sources.",
       "version": "0.0.0",
       "license": "",
       "creator": "",
@@ -4675,7 +4819,7 @@
     },
     {
       "name": "bio-workflows-chipseq-pipeline",
-      "description": "End-to-end ChIP-seq workflow from FASTQ files to annotated peaks. Covers QC, alignment, peak calling with MACS3, and peak annotation with ChIPseeker. Use when processing ChIP-seq data from alignment through peak annotation.",
+      "description": "End-to-end ChIP-seq workflow from FASTQ files to annotated peaks. Covers QC, alignment, peak calling with MACS3 (or HOMER), and peak annotation with ChIPseeker. Use when processing ChIP-seq data from alignment through peak annotation.",
       "version": "0.0.0",
       "license": "",
       "creator": "",
@@ -4685,6 +4829,18 @@
       "relPath": "workflows/chipseq-pipeline",
       "verified": true
     },
+    {
+      "name": "bio-workflows-clinical-trial-pipeline",
+      "description": "End-to-end clinical trial analysis workflow from CDISC data loading through statistical testing to regulatory-compliant reporting. Covers data preparation, logistic regression, categorical tests, subgroup analysis, and Table 1 generation. Use when performing a complete analysis of clinical trial data.",
+      "version": "0.0.0",
+      "license": "",
+      "creator": "",
+      "compatibility": "",
+      "allowedTools": [],
+      "installUrl": "github:GPTomics/bioSkills:workflows/clinical-trial-pipeline",
+      "relPath": "workflows/clinical-trial-pipeline",
+      "verified": true
+    },
     {
       "name": "bio-workflows-clip-pipeline",
       "description": "End-to-end CLIP-seq analysis from FASTQ to binding sites and motif enrichment. Use when analyzing protein-RNA interactions from CLIP-based methods.",
@@ -4987,7 +5143,7 @@
     },
     {
       "name": "bio-workflows-proteomics-pipeline",
-      "description": "End-to-end proteomics workflow from MaxQuant output to differential protein abundance. Orchestrates data import, normalization, imputation, and statistical testing with MSstats or limma. Use when processing mass spectrometry proteomics.",
+      "description": "End-to-end proteomics workflow from MaxQuant output to differential protein abundance. Orchestrates data import, normalization, imputation, and statistical testing with limma (default) or MSstats for complex feature-level designs. Use when processing mass spectrometry proteomics.",
       "version": "0.0.0",
       "license": "",
       "creator": "",

package/data/skill-index/Galaxy-Dawn_claude-scholar.json

@@ -2,8 +2,8 @@
   "repoUrl": "https://github.com/Galaxy-Dawn/claude-scholar.git",
   "owner": "Galaxy-Dawn",
   "repo": "claude-scholar",
-  "updatedAt": "2026-03-27T23:21:32.970Z",
-  "skillCount": 47,
+  "updatedAt": "2026-04-20T06:33:22.507Z",
+  "skillCount": 48,
   "skills": [
     {
       "name": "agent-identifier",
@@ -401,6 +401,18 @@
       "relPath": "skills/post-acceptance",
       "verified": true
     },
+    {
+      "name": "publication-chart-skill",
+      "description": "This skill should be used when the user asks for a publication-quality scientific figure or table, wants help choosing the right chart for results, needs a paper-ready pubfig or pubtab workflow, wants a figure + companion table for a results section, wants an Excel sheet turned into publication-ready LaTeX, or wants an existing scientific figure/table reviewed and upgraded.",
+      "version": "0.2.0",
+      "license": "",
+      "creator": "",
+      "compatibility": "",
+      "allowedTools": [],
+      "installUrl": "github:Galaxy-Dawn/claude-scholar:skills/publication-chart-skill",
+      "relPath": "skills/publication-chart-skill",
+      "verified": true
+    },
     {
       "name": "research-ideation",
       "description": "This skill should be used when the user asks to \"brainstorm research ideas\", \"use 5W1H framework\", \"identify research gaps\", \"conduct gap analysis\", \"start research project\", \"conduct literature review\", \"define research question\", \"select research method\", \"plan research\", or mentions research project initiation phase. Provides comprehensive guidance for research startup workflow from idea generation to planning.",