scientific-skills/Academic Writing/response-letter/SKILL.md
Helps organize reviewer comments and generate a standardized Word (.docx) response letter that maps each change to its exact location (page/paragraph/line). Use when revising a manuscript, replying to peer-review feedback, or preparing internal review responses.
npx skillsauth add aipoch/medical-research-skills response-letterInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
3 of 9 scanners reported clean
Some scanners were skipped, did not run, or reported a non-clean status. Review each row below.
.docx output (Word-compatible document generation)references/guide.mdInput:
- Manuscript (tracked version or clean version + change notes)
- Reviewer comments (all reviewers, all rounds)
- Current manuscript pagination/line numbering scheme (if available)
Steps:
1) Organize comments
- Merge all reviewer comments into a single list.
- Number them sequentially (e.g., R1-1, R1-2…; R2-1…).
- Tag each as Major or Minor.
2) Draft "Overview for the Editor"
- Write one concise paragraph summarizing the major revisions and their rationale.
3) Write point-by-point responses
For each numbered comment, output:
- Reviewer’s Comment: (verbatim or lightly cleaned for clarity)
- Response: (polite, direct, addresses the request)
- Changes in Text: (what changed + where)
4) Mark locations and quote revised text
- Provide page/paragraph/line for each change.
- Specify additions/deletions.
- Quote the revised paragraph when the main text is modified.
5) Generate deliverables
- Export the full response letter as a Word document (.docx).
- Produce a modification/execution checklist to verify all changes are applied.
Output (Word .docx structure):
- Title / Manuscript info (optional)
- Overview for the Editor
- Responses to Reviewer 1
- R1-1
- R1-2
...
- Responses to Reviewer 2
...
- Modification / Execution Checklist
R{reviewer}-{index}) to preserve traceability across revision rounds..docx).references/guide.md for required output formats, checklist items, and key writing points.tools
Generates complete conventional oncology bulk-transcriptome biomarker and hub-gene research designs from a user-provided cancer type and study direction. Always use this skill whenever a user wants to design, plan, or build a tumor bioinformatics study centered on differential expression, prognostic filtering or risk modeling, PPI-based hub-gene prioritization, diagnostic/prognostic evaluation, clinical association, immune infiltration context, methylation context, and optional tissue or cell validation. Covers five study patterns (signature-first prognostic workflow, hub-gene-first biomarker workflow, hybrid signature-to-hub workflow, immune-context biomarker workflow, translational validation workflow) and always outputs four workload configs (Lite / Standard / Advanced / Publication+) with recommended primary plan, step-by-step workflow, figure plan, validation strategy, minimal executable version, publication upgrade path...
development
Generates complete conventional non-oncology bioinformatics research designs from a user-provided disease context, process-related gene family or biological theme, and validation direction. Use when a study centers on multi-dataset bulk transcriptome integration, DEG analysis, process-gene intersection, enrichment analysis, GSEA, PPI hub-gene prioritization, TF/miRNA regulatory networks, ROC-based biomarker evaluation, and immune infiltration analysis. Covers five study patterns (process-DEG discovery, enrichment/GSEA interpretation, hub-gene prioritization, regulatory-network and immune interpretation, multi-layer public validation) and always outputs Lite / Standard / Advanced / Publication+ with a recommended primary plan, stepwise workflow, figure plan, validation hierarchy, minimal executable version, publication upgrade path, and strictly verified literature retrieval.
tools
Plans confounder control, variable adjustment logic, and bias mitigation strategies at the protocol stage for clinical, epidemiologic, translational, observational, and biomarker studies. Always use this skill when a user needs to identify major confounders, decide which variables should or should not be adjusted for, compare matching/stratification/weighting approaches, anticipate selection or measurement bias, or pressure-test a study design before execution. Focus on bias sensing, causal structure awareness, variable-role classification, and critical design review rather than generic statistical advice.
testing
Generates complete comparative network-toxicology research designs from a user-provided exposure pair, shared toxic phenotype, and validation direction. Use when a study centers on two related exposures under one outcome and needs target collection, shared-vs-specific target decomposition, enrichment, PPI hub prioritization, docking, optional transcriptomic cross-checks, and conservative mechanistic synthesis. Covers five study patterns and always outputs Lite / Standard / Advanced / Publication+ with a recommended primary plan, stepwise workflow, figure plan, validation hierarchy, minimal executable version, publication upgrade path, and strictly verified literature retrieval.