Explore AI Agent Skills & Claude Prompts

Process and visualize deep-sequencing coverage with the deepTools CLI — convert BAM to bigWig (bamCoverage), build log2 ratio tracks (bamCompare), run QC (multiBamSummary correlation, PCA, plotFingerprint), apply the ATAC-seq Tn5 shift (alignmentSieve --ATACshift), and make TSS/peak heatmaps and profiles (computeMatrix, plotHeatmap, plotProfile). Use for coverage tracks, signal heatmaps/profiles, normalization (RPGC/CPM/RPKM), and effective-genome-size lookups for ChIP-seq, ATAC-seq, MNase-seq, or RNA-seq. NOT for per-read/CIGAR/MAPQ BAM record access — that is pysam. Part of the AlterLab Academic Skills suite.

alterlab-latchbio

Builds and deploys bioinformatics pipelines on the LatchBio platform using the Latch SDK — author workflows with @workflow/@task decorators, handle LatchFile/LatchDir I/O, register serverless workflows, configure CPU/GPU task resources, organize data in the Latch Registry, and wrap Nextflow/Snakemake pipelines. Use when developing or deploying a Latch SDK workflow, sizing task resources, working with the Registry, or porting a Nextflow/Snakemake bioinformatics pipeline onto LatchBio. Not for DNAnexus (dxpy/dx CLI) or generic Flyte. Part of the AlterLab Academic Skills suite.

alterlab-fda

Query the openFDA API for drugs, medical devices, adverse event reports, recalls, regulatory submissions (510k, PMA), and substance identification (UNII). Use when searching FDA safety data, pharmacovigilance and adverse-event signals, device clearances, drug labels, or recall records for regulatory data analysis and safety research. Part of the AlterLab Academic Skills suite.

alterlab-thesis-supervisor

Supervises theses and dissertations end to end — structure guidance from proposal through defense, chapter-by-chapter writing support (introduction, literature review, methodology, results, discussion), supervision strategies, committee management, defense and viva voce preparation, timeline planning, feedback integration, examiner-expectation guidance, and formatting (APA 7, Chicago, university styles). Use when the request mentions thesis, dissertation, supervision, defense preparation, viva, proposal defense, thesis structure, thesis chapter, literature review chapter, methodology chapter, results chapter, discussion chapter, thesis timeline, committee, thesis formatting, or dissertation proposal. Part of the AlterLab Academic Skills suite.

alterlab-pyhealth

Develops, tests, and deploys clinical machine learning models with the PyHealth healthcare AI toolkit. Use when working with electronic health records (EHR), clinical prediction tasks (mortality, readmission, drug recommendation), medical coding systems (ICD, NDC, ATC), physiological signals (EEG, ECG), healthcare datasets (MIMIC-III/IV, eICU, OMOP), or implementing deep learning models for healthcare (RETAIN, SafeDrug, Transformer, GNN). Part of the AlterLab Academic Skills suite.

alterlab-astropy

Processes astronomy and astrophysics data with the Astropy Python library — celestial coordinates, physical units, FITS files, cosmological calculations, time systems, tables, and world coordinate systems (WCS). Use when tasks involve coordinate transformations, unit conversions, FITS file manipulation, cosmological distance calculations, time scale conversions, or general astronomical data analysis. Part of the AlterLab Academic Skills suite.

alterlab-zinc-db

Access the ZINC database of 230M+ commercially available (purchasable) compounds, searching by ZINC ID or SMILES, running similarity searches, and downloading 3D-ready structures. Use when assembling a compound library for virtual screening, finding purchasable analogs, or obtaining docking-ready 3D structures for drug discovery. Part of the AlterLab Academic Skills suite.

alterlab-anndata

Build, slice, concatenate, read, and write AnnData annotated data matrices (obs, var, X, layers, obsm, uns) for single-cell analysis in the scverse ecosystem. Use when handling .h5ad files, managing cell and gene annotations, or wrangling single-cell matrices — this is the data-format skill, for analysis workflows use scanpy, for probabilistic models use scvi-tools, for population-scale queries use cellxgene-census. Part of the AlterLab Academic Skills suite.

alterlab-opentrons

Writes liquid-handling protocols for Opentrons OT-2 and Flex robots using the official Opentrons Protocol API v2, with full access to v2 features for production-grade, officially compatible protocols. Use when authoring or running protocols specifically for Opentrons hardware. For multi-vendor automation or broader equipment control use pylabrobot instead. Part of the AlterLab Academic Skills suite.

alterlab-pylabrobot

Programs lab automation with PyLabRobot, a vendor-agnostic Python framework that unifies control across Hamilton, Tecan, Opentrons, plate readers, and pumps, with simulation support. Use when controlling multiple equipment types or needing unified cross-vendor programming for complex, multi-vendor liquid-handling workflows. For Opentrons-only protocols with the official API, alterlab-opentrons may be simpler. Part of the AlterLab Academic Skills suite.

alterlab-preregistration-discipline

Enforces pre-registration discipline with the Iron Law NO DATA ANALYSIS WITHOUT A PRE-REGISTERED ANALYSIS PLAN FIRST, a spirit-vs-letter line, an Excuse-vs-Reality rationalization table, and a Red-Flags-STOP list (HARKing, optional stopping, post-hoc covariates, outlier-dropping, test-shopping). Runs a PLAN/COLLECT/CONFIRM/EXPLORE workflow that freezes hypotheses, tests, exclusions, and stopping rules before data, then forces unplanned findings to be labeled exploratory (their p-values lose confirmatory status, per COS confirmatory/exploratory model). Orchestrates, not replaces, alterlab-open-science (OSF/AsPredicted registration), alterlab-statistical-analysis (test selection, assumptions), and alterlab-scientific-thinking (bias grading). Use when analyzing data without a frozen plan, switching the primary outcome or adding covariates after seeing results, weighing early stopping, dropping outliers post-hoc, pre-registering a study, or rationalizing deviation. Part of the AlterLab Academic Skills suite.

schedule Updated 14 days ago

alterlab-results-transparency

Enforces results-reporting transparency as a discipline gate built on the Iron Law "NO RESULTS CLAIM WITHOUT REPORTING EVERY ANALYSIS RUN" — a numbered Gate Function (IDENTIFY the claim, LIST every test actually run including the ones that did not "work", CHECK assumptions were reported, CHECK effect size with 95% CI is present, CHECK pre-registration deviations are disclosed, ONLY THEN write the sentence), plus an Excuse-vs-Reality table and Red-Flags-STOP list for selective reporting, cherry-picking, and bare p-values. Use when writing up Results, claiming a finding from a subset of analyses, reporting a p-value without an effect size or confidence interval, dropping outliers post hoc, or omitting analyses that did not pan out. Orchestrates alterlab-statistical-analysis (tests, effect sizes), alterlab-preregistration-discipline (the frozen plan), and alterlab-open-science (TOP, disclosure); it does not run the tests itself. Part of the AlterLab Academic Skills suite.