Research & Science · Python

Read, write, create, and convert single-cell objects across AnnData (Python), Seurat (R), and SingleCellExperiment (R).

GPTomics/bioSkills

Detect and remove doublets (two or more cells in one droplet) from single-cell RNA-seq using scDblFinder (R), Scrublet (Python), and DoubletFinder (R).

GPTomics/bioSkills

Detect cluster marker genes and assign manual cell type labels in single-cell RNA-seq using Scanpy (Python) and Seurat (R).

GPTomics/bioSkills

Quality control, ambient-RNA handling, normalization, and feature selection for single-cell RNA-seq using Scanpy (Python) and Seurat (R).

GPTomics/bioSkills

Analyze single-cell ATAC-seq with Signac/ArchR (R) and SnapATAC2 (Python alternative).

GPTomics/bioSkills

Segments cells/nuclei and extracts image features from imaging spatial transcriptomics (Xenium, MERFISH/MERSCOPE, CosMx) and H&E/IF tissue images using Cellpose, StarDist, Baysor, and Squidpy.

GPTomics/bioSkills

Measures geometric properties of protein structures with Biopython Bio.PDB - interatomic distances, distance matrices, bond and dihedral angles (phi/psi/chi, Ramachandran), superposition and RMSD…

GPTomics/bioSkills

Maps protein-protein and protein-ligand interfaces with Bio.PDB, computing contact residues and buried surface area (BSA).

GPTomics/bioSkills

Builds and simulates multi-species metabolic community models from member genome-scale models, using MICOM for abundance-weighted steady-state community FBA and cooperative tradeoff, SMETANA for…

GPTomics/bioSkills

Builds tissue-, cell-type-, and condition-specific metabolic models by integrating transcriptomic or proteomic data into a generic genome-scale model, using extraction algorithms (GIMME, iMAT…

GPTomics/bioSkills

Performs flux balance analysis (FBA), flux variability analysis (FVA), parsimonious FBA (pFBA), loopless FBA, flux sampling, and production envelopes on genome-scale metabolic models with COBRApy…

GPTomics/bioSkills

Performs in-silico single and double gene deletions, condition-dependent essentiality, and synthetic-lethality screens on genome-scale metabolic models with COBRApy, evaluating gene-protein-reaction…

GPTomics/bioSkills

Validates, gap-fills, and standardizes genome-scale metabolic models using memote for consistency and annotation scoring and COBRApy for manual curation, including mass/charge balance…

GPTomics/bioSkills

Computes metabolic-engineering strain designs on genome-scale models with StrainDesign (OptKnock, RobustKnock, minimal cut sets, OptCouple) and cameo (heuristic knockout and FSEOF…

GPTomics/bioSkills

Maps TCR/BCR receptor sequences toward candidate antigen specificity and clusters repertoires by shared-specificity signal, while enforcing that a database match or a cluster label is a HYPOTHESIS…

GPTomics/bioSkills

Infers directed, time-delayed gene regulatory edges from BULK time-series expression using Granger causality (statsmodels VAR F-test), dynGENIE3 (tree ensembles regressing ODE-derived derivatives…

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

Rigorous multi-pass editor for law review articles, student notes, seminar papers and other legal scholarship.

lawve-ai/awesome-legal-skills

This skill should be used when the user asks to "implement a DiD regression", "write a causal inference pipeline", "set up an event study", "implement instrumental variables", "run a regression…

brycewang-stanford/Auto-Empirical-Research-Skills

Inspect a registered execution server before compute planning and interpret its persisted capability profile.

xuzhougeng/wisp-science

Use Jacobian’s typed operations when exact computation or structural analysis can help solve a mathematical problem.

morluto/jacobian

How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval.

BioTender-max/awesome-bio-agent-skills

A skill your agent uses when the user wants to generate or edit images with Google's Nanobanana/Gemini image models using the official Gemini API shape, or when they need publication-style…

LeoYeAI/openclaw-master-skills

Unified CLI/Python interface to 20+ genomic databases. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Bulk RNA-seq DE with PyDESeq2: load counts, normalize, fit negative binomial models, Wald test (BH-FDR), LFC shrinkage, volcano/MA plots.

jaechang-hits/SciAgent-Skills

Symbolic math in Python: exact algebra, calculus (derivatives, integrals, limits), equation solving, symbolic matrices, ODEs, code gen (lambdify, C/Fortran).

jaechang-hits/SciAgent-Skills

Primary retained Python toolkit for molecular biology sequence work.

foryourhealth111-pixel/Vibe-Skills

Comprehensive cheat sheet for using the Pathling Python API.

aehrc/pathling

Applies ACMG/AMP 2015 framework with ClinGen SVI specifications, Tavtigian 2018/2020 Bayesian point system, Abou Tayoun 2018 PVS1 decision tree, Pejaver 2022 and Bergquist 2025 calibrated PP3/BP4…

GPTomics/bioSkills

Delimits putative species boundaries from molecular data within the de Queiroz 2007 unified-lineage framework using ASAP (Puillandre 2021 successor to ABGD), mPTP C++ (Kapli 2017 successor to bPTP…

GPTomics/bioSkills

Stores and operates on sparse expression matrices for single-cell and large bulk RNA-seq, covering dgCMatrix/dgRMatrix/dgTMatrix when-each-is-fast, the dgCMatrix (CSC, R) <- CSR (Python) implicit…

GPTomics/bioSkills

Nominates and assesses CRISPR off-target sites genome-wide. An agent skill from GPTomics/bioSkills.

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

Tests for differentially abundant proteins between conditions with limma/DEqMS empirical-Bayes moderation, proDA/msqrob2/MSstats missingness modeling, and Python Welch+BH alternatives.

GPTomics/bioSkills

Clusters temporally variable genes by expression-profile SHAPE (not significance) using Mfuzz fuzzy c-means, TCseq, DEGreport degPatterns, and tslearn DTW/soft-DTW.

GPTomics/bioSkills

End-to-end bulk time-course analysis from an expression matrix to temporal gene modules and per-cluster pathway enrichment.

GPTomics/bioSkills

A skill your agent uses when aer-identification has fixed the design, after methodology choice and before aer-robustness or aer-tables-figures, to run an AER-track analysis with StatsPAI — the…

brycewang-stanford/Auto-Empirical-Research-Skills

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

brycewang-stanford/Auto-Empirical-Research-Skills

Prepare a replication package for the sewage-house-prices project.

brycewang-stanford/Auto-Empirical-Research-Skills

Manual for the marginaleffects R and Python package, and guide to the book "Model to Meaning".

brycewang-stanford/Auto-Empirical-Research-Skills

Run the instrumented specification search in the user's own statistical language — Stata (reghdfe, ivreghdfe, rdrobust, did2s), R (fixest, rdrobust, did2s), Python (statsmodels, linearmodels) or…

brycewang-stanford/Auto-Empirical-Research-Skills

Dense, machine-readable API reference for PyFixest — high-dimensional fixed-effects OLS/WLS/IV and Poisson (feols, fepois, feglm), clustered/robust standard errors, R-style formula syntax, and…

brycewang-stanford/Auto-Empirical-Research-Skills

Stata-to-Python translation for data analysis. An agent skill from brycewang-stanford/Auto-Empirical-Research-Skills.

brycewang-stanford/Auto-Empirical-Research-Skills

Econometrics skill for creating publication-quality LaTeX regression and summary tables.

brycewang-stanford/Auto-Empirical-Research-Skills

Molecular docking with AutoDock Vina (Python API). An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Cheminformatics toolkit for molecular analysis and virtual screening: SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints (Morgan/ECFP, MACCS), Tanimoto similarity, SMARTS substructure…

jaechang-hits/SciAgent-Skills

scRNA-seq with Scanpy: QC, normalization, HVG selection, PCA, neighborhood graph, UMAP/t-SNE, Leiden clustering, markers, cell annotation, trajectory inference.

jaechang-hits/SciAgent-Skills

Check for interactions between multiple medications, including severity classification and mechanism explanations.

aipoch/medical-research-skills