alterlab-ieu/alterlab-academic-skills

1

alterlab-teaching-design Designs courses and teaching materials using backward design (Wiggins & McTighe), constructive alignment (Biggs), and…

alterlab-ieu/alterlab-academic-skills

92

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alterlab-literature-review Conducts comprehensive, systematic literature reviews across multiple academic databases (PubMed, arXiv, bioRxiv, Sem…

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73

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alterlab-thesis-supervisor Supervises theses and dissertations end to end — structure guidance from proposal through defense, chapter-by-chapter…

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73

4

alterlab-survey-design Comprehensive survey and instrument design assistant supporting questionnaire construction, Likert scale design, ques…

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68

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alterlab-social-science-methods Guides advanced social science research methods — discourse analysis (Fairclough CDA, Gee), conversation analysis, qu…

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alterlab-infographics Creates professional infographics with Nano Banana Pro AI and smart iterative refinement, using Gemini 3 Pro for auto…

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alterlab-matplotlib Builds plots with the matplotlib Python library (pyplot and the object-oriented Figure/Axes API) for full low-level c…

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63

8

alterlab-statsmodels Statistical modeling in Python with statsmodels — OLS, GLM, mixed models, and ARIMA with detailed diagnostics, residu…

alterlab-ieu/alterlab-academic-skills

63

9

alterlab-zarr Chunked, compressed N-dimensional arrays for cloud storage with Zarr — parallel I/O, S3/GCS integration, and NumPy/Da…

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63

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alterlab-arboreto Infer gene regulatory networks (GRNs) from expression matrices using arboreto's scalable GRNBoost2 and GENIE3 tree-en…

alterlab-ieu/alterlab-academic-skills

62

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alterlab-astropy Processes astronomy and astrophysics data with the Astropy Python library — celestial coordinates, physical units, FI…

alterlab-ieu/alterlab-academic-skills

62

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alterlab-clinical-reports Writes comprehensive clinical reports — case reports (CARE guidelines), diagnostic reports (radiology, pathology, lab…

alterlab-ieu/alterlab-academic-skills

62

13

alterlab-mixed-methods Mixed methods research design and integration strategies for combining qualitative and quantitative approaches. Use w…

alterlab-ieu/alterlab-academic-skills

62

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alterlab-open-science Guidance for open science practices — preregistration (OSF Registries, AsPredicted, PROSPERO, ClinicalTrials.gov), op…

alterlab-ieu/alterlab-academic-skills

62

15

alterlab-pptx-posters Creates research posters in HTML/CSS with responsive layouts and easy visual integration, exportable to PDF or PPTX. …

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62

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alterlab-pydeseq2 Run differential gene expression analysis on bulk RNA-seq count matrices with PyDESeq2, the Python port of DESeq2 — s…

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62

17

alterlab-research-ethics International research ethics and compliance assistant supporting IRB/ethics board applications, informed consent dra…

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62

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alterlab-scientific-schematics Creates publication-quality scientific diagrams with Nano Banana 2 AI and smart iterative refinement, using Gemini 3.…

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alterlab-seaborn Builds statistical plots with the seaborn Python library and pandas DataFrame integration, on attractive matplotlib-b…

alterlab-ieu/alterlab-academic-skills

62

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alterlab-statistical-analysis Guided statistical analysis with hypothesis-test selection, assumption checking, power analysis, and APA-formatted re…

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21

alterlab-academic-career Prepares academic career documents and professional-development materials for faculty and researchers. Use when draft…

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61

22

alterlab-alphafold-db Access the AlphaFold DB of 200M+ AI-PREDICTED protein structures — retrieve models by UniProt accession, download PDB…

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61

23

alterlab-biorxiv Search the bioRxiv preprint server and retrieve paper metadata or download PDFs via its API. Use when finding life sc…

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61

24

alterlab-cbioportal Query cBioPortal via its keyless REST API for cancer genomics across TCGA, GENIE, MSK-IMPACT and hundreds of studies …

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25

alterlab-deeptools Process and visualize deep-sequencing coverage with the deepTools CLI — convert BAM to bigWig (bamCoverage), build lo…

alterlab-ieu/alterlab-academic-skills

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26

alterlab-gget Run fast one-liner queries to 20+ bioinformatics databases from the gget CLI or Python — gene info (Ensembl), BLAST, …

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27

alterlab-latex-posters Creates professional research posters in LaTeX using beamerposter, tikzposter, or baposter — handles layout design, c…

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alterlab-phylogenetics Build phylogenetic trees end-to-end from raw sequences — MAFFT multiple sequence alignment, optional TrimAl trimming,…

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61

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alterlab-pubmed Provide direct REST API access to PubMed via the NCBI E-utilities API, supporting advanced Boolean/MeSH queries, batc…

alterlab-ieu/alterlab-academic-skills

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alterlab-qualitative-methods Comprehensive qualitative research methods assistant supporting thematic analysis (Braun & Clarke), grounded theory (…

alterlab-ieu/alterlab-academic-skills

61

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alterlab-tiledbvcf Store and query genomic variant data at scale with TileDB-VCF — ingest VCF/BCF into compressed TileDB arrays, add sam…

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alterlab-venue-templates Provides LaTeX templates, formatting requirements, and submission guidelines for major scientific venues (Nature, Sci…

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33

alterlab-anndata Build, slice, concatenate, read, and write AnnData annotated data matrices (obs, var, X, layers, obsm, uns) — the scv…

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34

alterlab-arxiv Search and retrieve preprints from arXiv via the Atom API by keywords, authors, arXiv IDs, date ranges, or subject ca…

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35

alterlab-biopython Manipulate biological sequences, parse FASTA/GenBank/PDB files, run phylogenetics, and access NCBI/PubMed programmati…

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36

alterlab-bioservices Query 40+ bioinformatics web services through one consistent Python API with bioservices (UniProt, KEGG, ChEMBL, Reac…

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37

alterlab-cellxgene Query the CZ CELLxGENE Census (61M+ cells) programmatically via cellxgene-census and TileDB-SOMA, slicing expression …

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alterlab-citation-mgmt Manages citations for academic research — searches Google Scholar and PubMed for papers, extracts accurate metadata, …

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alterlab-cobrapy Build and analyze genome-scale constraint-based metabolic models with COBRApy — flux balance analysis (FBA), flux var…

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alterlab-deep-research Runs a 13-agent deep research pipeline for rigorous academic work on any topic across 7 modes (full research, quick b…

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41

alterlab-depmap Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivi…

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alterlab-diffdock Predicts protein-ligand binding poses with DiffDock diffusion-based molecular docking from PDB structures and SMILES,…

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alterlab-digital-humanities Applies computational methods to humanities research — text mining and NLP (LDA/BERTopic topic modeling, sentiment, n…

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alterlab-eda Exploratory data analysis (EDA) on a scientific data file — auto-detects the format, runs structure/quality/statistic…

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alterlab-edgartools Accesses, analyzes, and extracts data from SEC EDGAR filings using the edgartools Python library. Use when working wi…

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46

alterlab-fred Queries the FRED (Federal Reserve Economic Data) API for 800,000+ economic time series from 100+ sources, covering GD…

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alterlab-generate-image Generates or edits raster images via AI models (FLUX.2, Gemini 3.1 Flash Image / "Nano Banana 2") through an OpenRout…

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alterlab-geo Access NCBI GEO (Gene Expression Omnibus) for gene expression and functional genomics data — search and download micr…

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alterlab-gwas Query the NHGRI-EBI GWAS Catalog REST API for SNP-trait associations, retrieving variants by rs ID, disease/trait, or…

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alterlab-molecular-dynamics Runs and analyzes molecular dynamics simulations with OpenMM and MDAnalysis — setting up protein and small-molecule s…

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