Best reproducible research skills, page 3

Tests a gene list (ORA, enrichWP) or a ranked gene vector (GSEA, gseWP) against the WikiPathways community-curated pathway collection with clusterProfiler and rWikiPathways.

GPTomics/bioSkills

Authors portable, strongly-typed bioinformatics pipelines in the Common Workflow Language (CWL v1.2) as CommandLineTool/Workflow/ExpressionTool documents, validated with cwltool and run at scale on…

GPTomics/bioSkills

Authors reproducible Nextflow DSL2 pipelines built on reactive dataflow, where processes communicate only through channels and execution order is not guaranteed.

GPTomics/bioSkills

Runs and configures curated nf-core community Nextflow pipelines (rnaseq, sarek, atacseq, methylseq, ampliseq, taxprofiler, fetchngs) reproducibly, pinning the pipeline revision with -r and…

GPTomics/bioSkills

Authors reproducible bioinformatics pipelines with Snakemake - rules wired by output-file pattern, wildcards and expand() for sample fan-out, checkpoints for runtime-unknown outputs, resource/retry…

GPTomics/bioSkills

Authors bioinformatics pipelines in WDL (Workflow Description Language) run by Cromwell or miniwdl, targeting the GATK/Broad and Terra/AnVIL/BioData Catalyst cloud ecosystem, with tasks, workflows…

GPTomics/bioSkills

Orchestrates the end-to-end ChIP-seq pipeline from FASTQ to blacklist-filtered, annotated peaks, chaining fastp QC, Bowtie2 alignment, pre-dedup library-complexity QC (NRF/PBC), duplicate removal…

GPTomics/bioSkills

Orchestrates an end-to-end MeRIP-seq / m6A-seq analysis from raw FASTQ to differential m6A peak calls and metagene plots, chaining fastp adapter trimming, STAR splice-aware alignment (NO…

GPTomics/bioSkills

This skill covers reproducible research pipelines and replication packages.

brycewang-stanford/Auto-Empirical-Research-Skills

Audit in-text citations, the reference list, appendices, code and supporting materials of a HUAWEI Cup paper, including reference consistency, appendix completeness, reproducibility and the 50MB…

xieyouxixi/hwb-math-modeling-skills

Interpret completed experimental outputs after host/runtime execution using pre-declared statistical tests, effect/uncertainty estimates, reproducibility checks, and calibrated synthesis.

yogsoth-ai/de-anthropocentric-research-engine

A skill your agent uses when handling data documentation, sharing, and spatial-data ethics for an Annals of the American Association of Geographers manuscript — provenance (sources, projections…

brycewang-stanford/Awesome-Journal-Skills

Transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M.

ClawBio/ClawBio

Wrapper skill for running nf-core/scrnaseq 4.1.0 upstream single-cell RNA-seq preprocessing from FASTQ with strict preflight, reproducibility outputs, and downstream handoff to ClawBio scRNA skills.

ClawBio/ClawBio

Open-source FAIR biology data framework. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Code review focused on experiment integrity, not general code quality.

appleweiping/WEIPING_WIKI

Evaluating scientific evidence and claims. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Adversarially audit changed analysis code against a base ref, hunting for correctness errors in sample construction, merges, variable construction, silent failures, and clustering or fixed effects.

claesbackman/AI-research-feedback

A skill your agent uses when refactoring research code for publication, adding documentation to existing analysis scripts, creating reproducible computational workflows, or preparing code for…

aipoch/medical-research-skills

Converts LabArchives notebook data, entry metadata, and authorized ELN exports into manuscript-ready academic writing outputs such as Methods sections, data-availability statements, reproducibility…

aipoch/medical-research-skills

Comprehensive reproducibility tool — audit Methods completeness for replication AND promote open science best practices (pre-registration, FAIR data, code sharing, replication design, reporting…

aipoch/medical-research-skills

Performs differential expression on bulk RNA-seq count data with edgeR's negative-binomial GLM and quasi-likelihood F-test framework.

GPTomics/bioSkills

Maps between gene identifier systems (Ensembl, Entrez, HGNC symbol, UniProt, RefSeq, MANE) using AnnotationDbi, biomaRt, mygene, pyensembl, and Ensembl REST.

GPTomics/bioSkills

Compares Hi-C contact maps between conditions across the right scale -- differential bin-pair contacts (multiHiCcompare, diffHic), differential A/B compartments (dcHiC), differential TAD boundaries…

GPTomics/bioSkills

Validate the replication package for the sewage-house-prices project.

brycewang-stanford/Auto-Empirical-Research-Skills

Publication Specialist - Writing, Review, Pre-registration & Quality Assurance Light VS applied: Avoids template-based writing + audience-specific message design Absorbed G3 (Peer Review…

brycewang-stanford/Auto-Empirical-Research-Skills

A skill your agent uses when starting empirical analysis, creating a data pipeline, generating results, or when data or model specifications change.

brycewang-stanford/Auto-Empirical-Research-Skills

R code review for the sewage project. An agent skill from brycewang-stanford/Auto-Empirical-Research-Skills.

brycewang-stanford/Auto-Empirical-Research-Skills

Think and work like an expert Experimental Physicist. An agent skill from K-Dense-AI/scientific-agents.

K-Dense-AI/scientific-agents

Exports sanitized metadata, parameters, reproducibility details, quality metrics, and optional review artifacts from Medical AI inference runs or evidence packs to MLflow.

NVIDIA/skills

Write and revise the Methods section of research papers to ensure reproducibility; use when preparing an IMRAD manuscript or responding to journal/reporting-guideline requirements (e.g…

aipoch/medical-research-skills

Evaluate the reproducibility of technical articles. An agent skill from mizchi/skills.

mizchi/skills

A skill your agent uses when a paper is complete or near-complete and a holistic pre-submission audit is needed.

brycewang-stanford/Auto-Empirical-Research-Skills

Scaffold a new research project with full reproducibility infrastructure in R and/or Python.

brycewang-stanford/Auto-Empirical-Research-Skills

Rigorous audit of experiment results before they become paper claims.

appleweiping/WEIPING_WIKI

Apply source-aware mechanical-engineering judgment to research, analysis, coding, writing, teaching, research identity, and release work.

hashgraph-online/awesome-codex-plugins

Produce a minimal Exa diagnostic bundle that preserves reproducibility without exposing credentials, queries, retrieved content, or customer data.

jeremylongshore/tons-of-skills-marketplace

Captures tool versions, packages, and kernel info as a reproducibility record in notes/.

brycewang-stanford/Auto-Empirical-Research-Skills

Systematic multi-agent code review of all analysis scripts produced in a project.

joshzyj/open-scholar-skill

Format, select, and prepare a manuscript for journal submission.

joshzyj/open-scholar-skill

Implement open science practices for a social science study.

joshzyj/open-scholar-skill

External review via OpenAI Codex CLI agents. An agent skill from joshzyj/open-scholar-skill.

joshzyj/open-scholar-skill

Structured, reproducible analysis documentation. An agent skill from nimrodfisher/data-analytics-skills.

nimrodfisher/data-analytics-skills

Structured peer review of manuscripts and grants. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Standardize fragmented experimental steps into reproducible protocol documents when you need method organization, lab SOP drafting, or cross-operator reproducibility; missing parameters must be…

aipoch/medical-research-skills

A skill your agent uses whenever you are reasoning about large-scale scientific projects, genomics, bioethics, data infrastructure, or long-term medical translation.

K-Dense-AI/mimeographs

Computational provenance audit verifying every number, table, and figure in a manuscript derives from code, not manual entry.

Mathews-Tom/armory

Verify technical nonfiction manuscripts for runnable accuracy, including commands, configuration, code snippets, links, version drift, screenshots, prerequisites, security warnings, expected…

hashgraph-online/awesome-codex-plugins