@yibeichan/claude-skills 1.0.2

package/skills/scientific-writer/references/reporting_guidelines.md

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+# Reporting Guidelines Reference
+
+## Contents
+1. [Guideline Selection](#guideline-selection)
+2. [CONSORT](#consort-randomized-trials)
+3. [STROBE](#strobe-observational-studies)
+4. [PRISMA](#prisma-systematic-reviews)
+5. [Other Guidelines](#other-guidelines)
+
+---
+
+## Guideline Selection
+
+| Study Type | Guideline | Website |
+|-----------|-----------|---------|
+| Randomized controlled trial | CONSORT | consort-statement.org |
+| Observational (cohort, case-control, cross-sectional) | STROBE | strobe-statement.org |
+| Systematic review/meta-analysis | PRISMA | prisma-statement.org |
+| Diagnostic accuracy | STARD | stard-statement.org |
+| Prediction models | TRIPOD | tripod-statement.org |
+| Animal research | ARRIVE | arriveguidelines.org |
+| Case reports | CARE | care-statement.org |
+| Quality improvement | SQUIRE | squire-statement.org |
+| Economic evaluation | CHEERS | ispor.org/cheers |
+| Clinical trial protocol | SPIRIT | spirit-statement.org |
+
+**Rule**: Identify applicable guideline before writing. Use checklist during drafting.
+
+---
+
+## CONSORT (Randomized Trials)
+
+### Essential Elements
+
+**Title/Abstract**
+- Identify as randomized trial in title
+- Structured abstract with trial design, methods, results, conclusions
+
+**Introduction**
+- Scientific background and rationale
+- Specific objectives or hypotheses
+
+**Methods**
+- Trial design (parallel, factorial, etc.) with allocation ratio
+- Eligibility criteria for participants
+- Settings and locations
+- Interventions with sufficient detail for replication
+- Pre-specified primary and secondary outcomes
+- Sample size calculation
+- Randomization: sequence generation, allocation concealment, implementation
+- Blinding: who was blinded, how
+
+**Results**
+- Flow diagram (REQUIRED): enrollment, allocation, follow-up, analysis
+- Baseline demographics table
+- Numbers analyzed per group
+- Primary outcome: effect estimate with precision (95% CI)
+- All pre-specified secondary outcomes
+- Harms/adverse events
+
+**Discussion**
+- Limitations (sources of bias, imprecision)
+- Generalizability
+- Interpretation consistent with results
+
+**Other**
+- Registration number and registry name
+- Protocol access
+- Funding source
+
+### CONSORT Flow Diagram
+```
+Enrollment:     Assessed for eligibility (n=)
+                    ↓
+                Excluded (n=)
+                • Not meeting criteria (n=)
+                • Declined (n=)
+                • Other (n=)
+                    ↓
+                Randomized (n=)
+                    ↓
+Allocation:     ←——————————————→
+                Intervention (n=)    Control (n=)
+                    ↓                    ↓
+Follow-up:      Lost to FU (n=)     Lost to FU (n=)
+                Discontinued (n=)    Discontinued (n=)
+                    ↓                    ↓
+Analysis:       Analyzed (n=)        Analyzed (n=)
+                Excluded (n=)        Excluded (n=)
+```
+
+---
+
+## STROBE (Observational Studies)
+
+### Essential Elements
+
+**Title/Abstract**
+- Indicate study design (cohort, case-control, cross-sectional)
+
+**Introduction**
+- Background/rationale
+- Objectives including pre-specified hypotheses
+
+**Methods**
+- Study design with key elements
+- Setting: locations, dates of recruitment/exposure/follow-up
+- Participants: eligibility, sources, selection methods
+- Variables: outcomes, exposures, predictors, confounders
+- Data sources/measurement for each variable
+- Bias: efforts to address potential sources
+- Study size: how determined
+- Statistical methods including confounding control
+
+**Results**
+- Participant flow diagram
+- Descriptive data: characteristics, exposures, follow-up time
+- Outcome data: numbers in each category
+- Main results: unadjusted and adjusted estimates with CI
+- Other analyses (subgroups, interactions, sensitivity)
+
+**Discussion**
+- Key results summary
+- Limitations including bias direction
+- Interpretation with literature context
+- Generalizability
+
+### Study-Specific Requirements
+
+**Cohort studies**: Report numbers at each follow-up stage, person-time at risk
+
+**Case-control studies**: Report case/control selection rationale, matching criteria
+
+**Cross-sectional studies**: Report analytical methods for sampling strategy
+
+---
+
+## PRISMA (Systematic Reviews)
+
+### Essential Elements
+
+**Title**
+- Identify as systematic review, meta-analysis, or both
+
+**Abstract**
+- Structured summary: background, objectives, data sources, eligibility, synthesis methods, results, limitations, conclusions, registration
+
+**Introduction**
+- Rationale and objectives (PICO format recommended)
+
+**Methods**
+- Protocol registration (PROSPERO, OSF)
+- Eligibility criteria
+- Information sources with dates
+- Search strategy (full for at least one database)
+- Selection process
+- Data collection process
+- Data items
+- Risk of bias assessment (tool used)
+- Effect measures
+- Synthesis methods (meta-analysis approach if used)
+- Certainty assessment (e.g., GRADE)
+
+**Results**
+- PRISMA flow diagram (REQUIRED)
+- Study characteristics
+- Risk of bias within studies
+- Results of individual studies
+- Synthesis results with heterogeneity
+- Risk of bias across studies
+- Certainty of evidence
+
+**Discussion**
+- Summary of evidence
+- Limitations
+- Conclusions
+
+### PRISMA Flow Diagram
+```
+Identification:  Records from databases (n=)
+                 Records from other sources (n=)
+                        ↓
+                 Records after duplicates removed (n=)
+                        ↓
+Screening:       Records screened (n=)
+                        ↓
+                 Records excluded (n=)
+                        ↓
+                 Full-text assessed (n=)
+                        ↓
+                 Full-text excluded (n=)
+                 • Reason 1 (n=)
+                 • Reason 2 (n=)
+                        ↓
+Included:        Studies in qualitative synthesis (n=)
+                        ↓
+                 Studies in meta-analysis (n=)
+```
+
+---
+
+## Other Guidelines
+
+### STARD (Diagnostic Accuracy)
+Key elements: Index test, reference standard, participant flow, 2×2 table, sensitivity/specificity with CI
+
+### TRIPOD (Prediction Models)
+Key elements: Model development vs. validation, predictor selection, model performance measures, calibration, discrimination
+
+### ARRIVE (Animal Research)
+Key elements: Species/strain, housing, sample size justification, randomization, blinding, humane endpoints
+
+### CARE (Case Reports)
+Key elements: Patient information, clinical findings, timeline, diagnostic assessment, therapeutic interventions, outcomes
+
+---
+
+## Pre-Submission Checklist
+
+- [ ] Correct guideline identified for study type
+- [ ] Checklist downloaded from official website
+- [ ] All applicable items addressed
+- [ ] Flow diagram included (CONSORT, STROBE, PRISMA)
+- [ ] Registration number included (trials, systematic reviews)
+- [ ] Checklist completed and ready for submission

package/skills.json

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+{
+  "$schema": "https://skills.anthropic.com/schema/v1",
+  "name": "claude-skills",
+  "version": "1.0.0",
+  "description": "Claude skills for neuroimaging research workflows and scientific writing",
+  "repository": "https://github.com/yibeichen/claude-skills",
+  "skills": [
+    {
+      "name": "bidsapp-nidm-standards",
+      "version": "1.0.0",
+      "description": "Standards for creating NIDM-integrated BIDSapps that run through BABS. Trigger keywords: BIDSapp, NIDM, BABS, FreeSurfer, repository structure",
+      "path": "skills/bidsapp-nidm-standards",
+      "author": "Yibei Chen",
+      "tags": ["neuroimaging", "BIDS", "NIDM", "BABS", "BIDSapp"],
+      "dependencies": []
+    },
+    {
+      "name": "neuroimaging-qc",
+      "version": "1.0.0",
+      "description": "Evidence-based QC decision-making for neuroimaging data (fMRI, EEG, fNIRS, structural MRI). Interpret QC metrics from fMRIPrep, MRIQC, FreeSurfer, MNE-Python, Homer3 to make justified inclusion/exclusion decisions. Trigger keywords: QC, quality control, fMRIPrep, MRIQC, motion, exclusion, subject filtering",
+      "path": "skills/neuroimaging-qc",
+      "author": "Yibei Chen",
+      "tags": ["neuroimaging", "QC", "fMRI", "EEG", "fNIRS", "quality-control"],
+      "dependencies": []
+    },
+    {
+      "name": "fmri-ssm",
+      "version": "1.0.0",
+      "description": "State-space models (SSMs) for fMRI analysis: HMM, HMM-MAR, sticky/HDP-HMM, IO-HMM, SLDS, rSLDS, SNLDS. Covers resting-state, task-based (MID, SST, N-back), and naturalistic fMRI. Trigger keywords: HMM on brain data, brain state dynamics, dynamic FC, switching dynamics, latent states from BOLD, SLDS on neural timeseries, fMRI state-space modeling",
+      "path": "skills/fmri-ssm",
+      "author": "Yibei Chen",
+      "tags": ["neuroimaging", "fMRI", "HMM", "state-space", "brain-dynamics", "SSM", "resting-state"],
+      "dependencies": []
+    },
+    {
+      "name": "dicom2fmriprep",
+      "version": "1.0.0",
+      "description": "Generate scripts for the full fMRI preprocessing pipeline: DICOM to BIDS conversion (heudiconv), BIDS validation, fMRIPrep with Singularity, and large-scale HPC processing via BABS on SLURM. Trigger keywords: DICOM, BIDS, heudiconv, fMRIPrep, BABS, SLURM, preprocessing, dcm2niix, heuristic",
+      "path": "skills/dicom2fmriprep",
+      "author": "Yibei Chen",
+      "tags": ["neuroimaging", "fMRI", "BIDS", "fMRIPrep", "heudiconv", "BABS", "SLURM", "preprocessing"],
+      "dependencies": []
+    },
+    {
+      "name": "scientific-writer",
+      "version": "1.0.0",
+      "description": "Write rigorous scientific manuscripts following academic standards (IMRAD, citations, figures, CONSORT/STROBE/PRISMA guidelines). Trigger keywords: scientific writing, research papers, grant proposals, literature reviews",
+      "path": "skills/scientific-writer",
+      "author": "Yibei Chen",
+      "tags": ["writing", "research", "academic", "publications"],
+      "dependencies": []
+    }
+  ]
+}