Samuel Nord
Community@mrsonord2240
Biomedical research skill registry spanning CRISPR screens, omics pipelines, Mendelian randomization, clinical trial design, and manuscript integrity auditing.
Agent Skills by Samuel Nord
Showing 142 vetted skills indexed across 1 GitHub repositories.
mrsonord2240figure-first-paper-reader
Reads research papers figure by figure to audit whether visuals support the authors' claims.
mrsonord2240high-value-paper-screener
Screens biomedical papers to recommend full read, skim, or skip decisions.
mrsonord2240contradictory-findings-resolver
Analyzes why biomedical studies on the same topic reach conflicting conclusions.
mrsonord2240reporting-guideline-compliance-checker
Checks biomedical manuscripts against CONSORT, STROBE, PRISMA, and TRIPOD reporting guidelines.
mrsonord2240methods-reverse-engineer
Reconstructs biomedical paper methods into ordered, reproducibility-audited workflow checklists.
mrsonord2240result-reliability-checker
Audits biomedical study results for design integrity, statistical risk, validation strength, and claim overreach.
mrsonord2240scientific-critical-thinking
Evaluate research methodology, statistical validity, biases, and evidence quality using GRADE and Cochrane ROB frameworks.
mrsonord2240rct-bias-assessment-rob2
Assess risk of bias in randomized controlled trials using the ROB2 framework.
mrsonord2240diagnostic-study-quality-assessment-quadas-2
Assesses diagnostic accuracy studies for bias using the QUADAS-2 framework.
mrsonord2240medical-research-literature-reader-pro
Analyzes medical research papers with track-routed critical appraisal and structured evidence reports.
mrsonord2240retraction-watcher
Scan reference lists and detect retracted, corrected, or flagged papers via Crossref and PubMed APIs.
mrsonord2240study-design-identifier
Identifies the real study design of biomedical papers from methods structure.
mrsonord2240reproducibility-check
Audits Methods sections for replication completeness and guides open science practices.
mrsonord2240paper-to-claim-verifier
Verifies whether scientific claims are supported by their cited primary papers.
mrsonord2240bio-crispr-screens-base-editing-analysis
Analyzes base-editing CRISPR screens for variant function using CRISPResso2 and MAGeCK.
mrsonord2240bio-crispr-screens-library-design
Designs pooled sgRNA libraries for CRISPR knockout, CRISPRi, CRISPRa, Cas12a, and editor screens.
mrsonord2240bio-crispr-screens-batch-correction
Diagnose and correct batch effects in pooled CRISPR screens using ComBat, RUV, SVA, and covariate modeling.
mrsonord2240bio-crispr-screens-jacks-analysis
Runs JACKS Bayesian joint analysis of CRISPR screens to estimate gene essentiality and guide efficacy.
mrsonord2240bio-workflows-crispr-screen-pipeline
Analyzes pooled and single-cell CRISPR screens from FASTQ to consensus hit genes.
mrsonord2240bio-crispr-screens-crispresso-editing
Quantifies CRISPR editing outcomes from amplicon sequencing using CRISPResso2 across Cas9, base editor, and prime editor modes.
mrsonord2240bio-crispr-screens-copy-number-correction
Corrects copy-number artifacts in cancer cell line CRISPR-Cas9 screens using CRISPRcleanR and Chronos.
mrsonord2240bio-pathway-gsea
Runs preranked GSEA on ranked gene vectors against GO, KEGG, Reactome, and MSigDB gene sets.
mrsonord2240bio-crispr-screens-hit-calling
Selects and reconciles statistical methods for calling hits in pooled CRISPR screens.
mrsonord2240bio-crispr-screens-bagel-essentiality
Identifies essential genes from CRISPR-Cas9 fitness screens using BAGEL2 Bayes Factors.
Frequently Asked Questions About Samuel Nord
FAQPage SchemaWhat tasks can I accomplish with Samuel Nord's skill registry?▼
You can run end-to-end CRISPR screen analysis, untargeted LC-MS metabolomics and DIA proteomics pipelines, Mendelian randomization and colocalization study designs, clinical trial protocol generation, survival and biomarker modeling, phylogenetic inference, and manuscript integrity checks including retraction scanning and reporting-guideline compliance.
Who are these skills designed for?▼
Bioinformaticians, computational biologists, clinical researchers, epidemiologists, and translational scientists. Skills assume familiarity with omics data formats (FASTQ, mzML, expression matrices), GWAS summary statistics, and biomedical manuscript conventions, targeting users preparing publications or designing studies.
What tools and runtimes do the analysis skills depend on?▼
Skills orchestrate established packages: MAGeCK, BAGEL2, drugZ, JACKS, CRISPResso2, and CRISPRcleanR for screens; xcms, MS-DIAL, matchms, and MetaboAnalystR for metabolomics; DIA-NN, MSstats, and limma for proteomics; clusterProfiler for enrichment; IQ-TREE2, BEAST2, and ASTRAL for phylogenetics, across R and Python environments.
Are these skills free to use and under what license?▼
Yes. The skills carry MIT licenses where specified, authored primarily by AIPOCH. They are prompt-level skill definitions that wrap open-source scientific software; the underlying tools (MAGeCK, xcms, DIA-NN, etc.) retain their own respective licenses.
How do the research-planner skills structure their output?▼
Planner skills generate complete study designs from a user-provided direction, outputting four workload tiers (Lite, Standard, Advanced, Publication+) with a recommended primary plan, stepwise workflow, figure plan, validation strategy, minimal executable version, and a verified reference layer that prohibits fabricated citations.