crazymsn/academic-scholar-skills
Skill Claude CodeCodex
Universal deep research agent team. 13-agent pipeline for rigorous academic research on any topic. 7 modes: full research, quick brief, paper review, lit-review, fact-check, Socratic guided research dialogue, and systematic review with optional meta-analysis. Covers research question formulation, Socratic mentoring…
crazymsn/academic-scholar-skills
Agent
Systematic literature search and curation; identifies, annotates, and formats sources in APA 7.0.
crazymsn/academic-scholar-skills
Agent
Challenges assumptions, tests logical chains, and stress-tests research arguments at mandatory checkpoints.
crazymsn/academic-scholar-skills
Agent
Q1 journal editorial review; delivers Accept/Reject verdict with actionable feedback on research reports.
crazymsn/academic-scholar-skills
Agent
Research ethics gate; ensures AI-assisted research meets attribution, disclosure, and integrity standards before delivery.
crazymsn/academic-scholar-skills
Agent
Quantitative synthesis of included studies; computes effect sizes, assesses heterogeneity, and applies GRADE framework.
crazymsn/academic-scholar-skills
Agent
Post-research literature monitoring; helps users track new publications and developments after a research project is complete.
crazymsn/academic-scholar-skills
Agent
Transforms vague topics into precise, FINER-evaluated researchable questions through iterative refinement.
crazymsn/academic-scholar-skills
Agent
Assesses risk of bias in included studies using RoB 2 (RCTs) and ROBINS-I (non-randomized studies).
crazymsn/academic-scholar-skills
Agent
Grades evidence, detects predatory publications, and fact-checks claims entering the research pipeline.
crazymsn/academic-scholar-skills
Agent
Extracts per-source temporal facts and citation provenance into Phase 2 sidecar artifacts; activated in Phase 2 (Investigation).
crazymsn/academic-scholar-skills
Hook
Runs when a session starts, executing announce-ars-loaded.sh via bash. From crazymsn/academic-scholar-skills.
Skill Claude CodeCodex
How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval. Use this skill whenever the user mentions Adaptyv, Foundry API, protein binding assays, protein screening experiments, BLI/SPR assays, thermostability assays, or wants to submit protein sequences for…
Skill Claude CodeCodex
This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorithms beyond standard…
Skill Claude CodeCodex
Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.
Skill Claude CodeCodex
Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for…
Skill Claude CodeCodex
Comprehensive Python library for astronomy and astrophysics. This skill should be used when working with astronomical data including celestial coordinates, physical units, FITS files, cosmological calculations, time systems, tables, world coordinate systems (WCS), and astronomical data analysis. Use when tasks involve…
Skill Claude CodeCodex
Observe the user's screen via screenpipe, detect repeated research workflows, match them against existing academic-skills, and draft new skills (or composition recipes that chain existing ones) for the patterns not yet covered. Use when the user asks to analyze their recent work and propose skills based on what they…
Skill Claude CodeCodex
Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.
Skill Claude CodeCodex
Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server. Returns 25+ fields per paper including methods, results, sample sizes, quality scores, and conclusions. Use for literature reviews, evidence synthesis, and finding experimental details not…
Skill Claude CodeCodex
Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, motion capture, EMG, MR spectroscopy, behavioral), querying BIDS layouts, validating compliance, converting DICOM to BIDS, writing metadata sidecars…
Skill Claude CodeCodex
Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use…
Skill Claude CodeCodex
Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use…
Skill Claude CodeCodex
Query the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues, diseases, or cell types from the largest curated single-cell atlas. Best for population-scale queries, reference atlas comparisons. For analyzing your own data use scanpy or scvi-tools.