Agent skill

Methods Section Guide

by wentorai in wentorai/research-plugins

Guide to writing clear and reproducible methodology sections

MITAuto-check passedData & Analytics

Install Methods Section Guide

skills CLI
$ npx skills add wentorai/research-plugins --skill methods-section-guide -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install wentorai/research-plugins methods-section-guide --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/writing/composition/methods-section-guide .claude/skills/methods-section-guide && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
methods-section-guide
GitHub stars
298
Used in
1 other repo
Token cost
~1.9k tokens
SKILL.md length
451 words
Files
1
Skills in repo
428
Repo updated
First seen
Licence
MIT

At a glance

Guide to writing clear and reproducible methodology sections

  • Tasks that involve Experimental design
  • SKILL.md covers Purpose of the Methods Section, Standard Structure, Writing by Discipline and Reproducibility Checklist, plus 2 more sections
  • Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Methods Section Guide is an agent skill from wentorai/research-plugins. Guide to writing clear and reproducible methodology sections

Its SKILL.md is about 1.9k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Data & Analytics, covering Experimental design. The repository describes itself as: 350+ academic research skills, MCP configs, and plugins for Research-Claw and AI agents. The licence is MIT.

When your agent uses it

  • Tasks that involve Experimental design

Example prompts

  • “/methods-section-guide”

What it can do on your machine

Read from SKILL.md and the folder at commit bf44b3c. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    No scripts in the folder and no shell commands in SKILL.md (its code samples are markdown).

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Methods Section Guide loads about 1.9k tokens when it runs. Until then it costs about 21 tokens; SKILL.md has 451 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~21
When it runs · the whole SKILL.md, loaded when a task matches
~1.9k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from wentorai/research-plugins at commit bf44b3c, republished under its MIT licence (© wentorai). 451 words, ~1,919 tokens.

Download SKILL.mdSave it as .claude/skills/methods-section-guide/SKILL.md (or your agent's skills folder).
name
methods-section-guide
description
Guide to writing clear and reproducible methodology sections

Methods Section Writing Guide

Write methodology sections that are clear, complete, and reproducible, following discipline-specific conventions and best practices.

Purpose of the Methods Section

The methods section answers: "How did you do this study, and can someone else replicate it?" A well-written methods section:

  • Provides enough detail for replication by an independent researcher
  • Justifies why each method was chosen
  • Describes the study design, participants, materials, and procedures
  • Specifies statistical or analytical approaches
  • Addresses ethical considerations

Standard Structure

The methods section typically follows this order (adapt to your discipline):

SubsectionContents
Study DesignOverall approach (experimental, observational, computational, qualitative)
Participants / SamplesPopulation, sampling strategy, inclusion/exclusion criteria, sample size justification
Materials / InstrumentsEquipment, software, reagents, questionnaires, datasets
ProcedureStep-by-step protocol, chronological order of data collection
Data AnalysisStatistical tests, software, significance thresholds, model specifications
Ethical ConsiderationsIRB approval, informed consent, data privacy

Writing by Discipline

Experimental Sciences (Biology, Chemistry, Physics)
markdown
## Materials and Methods

### Cell Culture and Treatment
HeLa cells (ATCC CCL-2) were maintained in DMEM (Gibco, #11965092)
supplemented with 10% FBS (Gibco, #26140079) and 1% penicillin-
streptomycin (Gibco, #15140122) at 37C in 5% CO2. Cells were
seeded at 5 x 10^4 cells/well in 24-well plates and treated with
compound X (0.1, 1, 10 uM) for 24 hours.

### Western Blot Analysis
Total protein was extracted using RIPA buffer (Thermo, #89900)
with protease inhibitor cocktail (Roche, #04693116001). Proteins
(30 ug/lane) were separated on 10% SDS-PAGE gels and transferred
to PVDF membranes. Primary antibodies: anti-TargetProtein
(Cell Signaling, #1234, 1:1000), anti-beta-actin (Sigma, #A5441,
1:5000). Secondary antibodies: HRP-conjugated (1:10000).

Key conventions:

  • Include catalog numbers for all reagents
  • Specify concentrations, temperatures, durations, and instrument models
  • Reference established protocols by citation rather than rewriting them in full
  • Use past tense throughout
Computational / Machine Learning Studies
markdown
## Methods

### Dataset
We evaluated our method on three benchmark datasets:
- **ImageNet-1K** (Russakovsky et al., 2015): 1.28M training images,
  50K validation images across 1,000 classes
- **CIFAR-100** (Krizhevsky, 2009): 50K training, 10K test, 100 classes
- **Oxford Flowers-102** (Nilsback & Zisserman, 2008): 8,189 images, 102 classes

### Model Architecture
Our model extends the Vision Transformer (ViT-B/16) with the
following modifications:
1. Replaced standard self-attention with linear attention (Katharopoulos et al., 2020)
2. Added a learnable class-conditional normalization layer after each block
3. Used patch size 16x16 with input resolution 224x224

### Training Details
| Hyperparameter | Value |
|---------------|-------|
| Optimizer | AdamW (beta1=0.9, beta2=0.999) |
| Learning rate | 1e-3 with cosine decay |
| Weight decay | 0.05 |
| Batch size | 256 (across 4 A100 GPUs) |
| Training epochs | 300 |
| Warmup epochs | 10 |
| Data augmentation | RandAugment (N=2, M=9), Mixup (alpha=0.8) |
| Label smoothing | 0.1 |

All experiments were implemented in PyTorch 2.1 and run on 4x NVIDIA A100
80GB GPUs. Training took approximately 18 hours per run. Code is available
at [repository URL].
Social Science / Survey Research
markdown
## Methods

### Participants
A total of 412 participants (245 female, 162 male, 5 non-binary;
M_age = 34.2, SD = 11.8) were recruited via Prolific. Inclusion
criteria: (a) aged 18-65, (b) fluent in English, (c) resided in
the US. Exclusion criteria: (a) failed two or more attention checks,
(b) completed the survey in under 3 minutes. After exclusions,
387 participants remained (attrition: 6.1%).

Sample size was determined a priori using G*Power 3.1 (Faul et al., 2007).
For a medium effect size (f^2 = 0.15), alpha = .05, and power = .80
in a multiple regression with 5 predictors, the required sample was 92.
We oversampled to ensure adequate power for subgroup analyses.

### Measures

**Perceived Stress Scale (PSS-10)** (Cohen et al., 1983): 10 items,
5-point Likert scale (0 = never, 4 = very often). Cronbach's alpha
in the current sample: .87.

**Big Five Inventory (BFI-10)** (Rammstedt & John, 2007): 10 items,
5-point Likert scale. Subscale alphas ranged from .68 to .81.

### Procedure
After providing informed consent, participants completed measures in
the following fixed order: demographics, PSS-10, BFI-10, experimental
task, manipulation check, debriefing. Median completion time: 14 minutes.
Participants were compensated GBP 2.50.

### Ethical Approval
This study was approved by the [University] IRB (Protocol #2024-0123).
All participants provided informed consent.

Reproducibility Checklist

Use this checklist to ensure your methods section is complete:

For All Studies
  • Study design and rationale clearly stated
  • Sample/dataset described with inclusion/exclusion criteria
  • Sample size justified (power analysis, saturation, or convention)
  • All measures and instruments described with psychometric properties or specifications
  • Procedure described in chronological order with enough detail for replication
  • Statistical/analytical methods specified, including software and version
  • Significance level (alpha) stated
  • Missing data handling described
  • Ethical approval and consent documented
Show full SKILL.md (191 more words)Show less
For Computational Studies
  • Hardware specifications (GPU model, memory, training time)
  • Software framework and version (PyTorch 2.1, TensorFlow 2.15, etc.)
  • All hyperparameters listed in a table
  • Random seed policy described
  • Code and data availability statement
  • Evaluation metrics defined precisely
  • Baseline methods described or cited

Common Pitfalls

IssueExampleFix
Vague descriptions"Data was analyzed statistically"Specify exact tests: "We used a two-tailed independent samples t-test"
Missing software versions"Analysis done in R""Analysis conducted in R 4.3.1 using lme4 v1.1-35"
No sample size justificationJust reporting NInclude power analysis or justify based on conventions
Ambiguous orderReader cannot tell what happened whenUse numbered steps or chronological narrative
Results in methodsIncluding p-values or outcomesSave all results for the Results section
Over-referencingCiting a protocol without summarizing key detailsProvide enough detail to understand without reading the reference

Language and Tense

  • Use past tense for what you did: "Participants completed a questionnaire..."
  • Use present tense for established methods: "ANOVA tests for differences between group means..."
  • Use passive voice when the agent is unimportant: "Samples were centrifuged at 12,000 rpm..."
  • Use active voice when clarity is improved: "We excluded participants who..."

© wentorai, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

Just SKILL.md in skills/writing/composition/methods-section-guide of wentorai/research-plugins.

Open the folder on GitHubat commit bf44b3c

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in wentorai/research-plugins, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Methods Section Guide next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Methods Section Guide compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Methods Section Guide this skillwentorai/research-plugins2981 repos~1.9kAutomated safety check: PassMIT
Statistical Powerspacering-net/codeg3.8k1 repos~3.6kAutomated safety check: NotesMIT
Research Methodologychekusu/wanman688—~533Automated safety check: PassApache-2.0
Research Data Feasibility and Leakage ChecksLight0305/Light-skills640—~4.9kAutomated safety check: PassMIT
Statistical Analystalirezarezvani/claude-skills28k1 repos~2.5kAutomated safety check: PassMIT
Bayesian Estimationbrycewang-stanford/Auto-Empirical-Research-Skills4.5k—~3.4kAutomated safety check: PassCustom licence

Similar skills

  • Statistical Power

    spacering-net/codeg

    Sample-size and statistical power calculations for planning studies.

    3.8k GitHub starsUsed in 1 repo~3.6k tokens
    Data & AnalyticsAuto-check: notes
  • Research Methodology

    chekusu/wanman

    Methodology for market research and data collection, ensuring data quality and source traceability

    688 GitHub stars~533 tokensUpdated 3 mo ago
    Data & AnalyticsAuto-check passed
  • Finds usable public datasets, judges whether the data can support a research idea, and checks train and test splits for leakage before results are trusted.

    640 GitHub stars~4.9k tokensUpdated 3 mo ago
    Data & AnalyticsAuto-check passed
  • Statistical Analyst

    alirezarezvani/claude-skills

    Run hypothesis tests, analyze A/B experiment results, calculate sample sizes, and interpret statistical significance with effect sizes.

    28k GitHub starsUsed in 1 repo~2.5k tokens
    Data & AnalyticsAuto-check passed
  • Bayesian Estimation

    brycewang-stanford/Auto-Empirical-Research-Skills

    This skill covers Bayesian estimation and inference in quantitative social science.

    4.5k GitHub stars~3.4k tokensUpdated 2 days ago
    Data & AnalyticsAuto-check passed
  • Power Analysis

    gaasher/Agent-Loop-Skills

    A skill your agent uses when the user is planning a two-arm comparison (an A/B test, a simple RCT, a behavioral study, or a two-model/two-config evaluation) and needs to size it and preregister it…

    174 GitHub stars~2.2k tokensUpdated 3 mo ago
    Data & AnalyticsAuto-check passed

More from wentorai/research-plugins

All 428 skills in this repo
  • Abstract Writing Guide

    wentorai/research-plugins

    Craft structured research abstracts that maximize clarity and journal acceptance

    298 GitHub starsUsed in 1 repo~1.7k tokens
    Auto-check passed
  • Academic Citation Manager

    wentorai/research-plugins

    Manage academic citations across BibTeX, APA, MLA, and Chicago formats

    298 GitHub starsUsed in 1 repo~2.7k tokens
    Auto-check passed
  • Academic Paper Summarizer

    wentorai/research-plugins

    Summarize academic papers with structured extraction of key elements

    298 GitHub starsUsed in 1 repo~1.4k tokens
    Auto-check passed
  • Academic Study Methods

    wentorai/research-plugins

    Evidence-based study techniques for academic learning and retention

    298 GitHub starsUsed in 1 repo~1.8k tokens
    Auto-check passed
  • Academic Tone Guide

    wentorai/research-plugins

    Adjust writing tone and register for academic audiences and venues

    298 GitHub starsUsed in 1 repo~1.9k tokens
    Auto-check passed
  • Academic Translation Guide

    wentorai/research-plugins

    Academic translation, post-editing, and Chinglish correction guide

    298 GitHub starsUsed in 1 repo~1.6k tokens
    Auto-check passed

Questions about Methods Section Guide

What does Methods Section Guide do?

Guide to writing clear and reproducible methodology sections. Methods Section Guide is an agent skill from wentorai/research-plugins.

When should I use Methods Section Guide?

Methods Section Guide fits situations like: tasks that involve Experimental design.

How do I install Methods Section Guide in Claude Code?

Run `npx skills add wentorai/research-plugins --skill methods-section-guide -a claude-code`. Or copy the skill folder (skills/writing/composition/methods-section-guide in wentorai/research-plugins) into .claude/skills/methods-section-guide in your project. Claude Code loads it when a task matches its description.

How do I install Methods Section Guide in Codex?

Run `npx skills add wentorai/research-plugins --skill methods-section-guide -a codex`. Or copy the skill folder (skills/writing/composition/methods-section-guide in wentorai/research-plugins) into .agents/skills/methods-section-guide in your project. Codex loads it when a task matches its description.

Can I use Methods Section Guide in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add wentorai/research-plugins --skill methods-section-guide -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/methods-section-guide, .gemini/skills/methods-section-guide, .github/skills/methods-section-guide and .opencode/skills/methods-section-guide in your project.

What does Methods Section Guide need to run?

SKILL.md names no scripts, command-line tools or credentials: Methods Section Guide is instructions for the agent only.

Does Methods Section Guide access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Methods Section Guide safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Methods Section Guide use?

Methods Section Guide is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Methods Section Guide use?

About 1.9k tokens (SKILL.md is roughly 7.7k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Methods Section Guide?

Skills that share tags, products or a category with Methods Section Guide: Statistical Power (spacering-net/codeg, 3.8k stars), Research Methodology (chekusu/wanman, 688 stars), Research Data Feasibility and Leakage Checks (Light0305/Light-skills, 640 stars) and Statistical Analyst (alirezarezvani/claude-skills, 28k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Methods Section Guide?

wentorai (a GitHub user) maintains it in wentorai/research-plugins, which has 298 GitHub stars. The repository holds 428 skills in this directory. The repository was last updated on June 19, 2026.

Source: wentorai/research-plugins on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.