Data & Analytics

A skill your agent uses when performing sample-level dimensionality reduction and visualization on abundance or OTU-style matrices with a companion group file, generating UMAP and/or t-SNE…

aipoch/medical-research-skills

A skill your agent uses when running prognostic survival analysis on a clinical cohort with time-to-event data to estimate univariate and multivariable Cox proportional hazards models, export result…

aipoch/medical-research-skills

A skill your agent uses when building XGBoost models on tabular data and returning feature importance ranking outputs.

aipoch/medical-research-skills

A skill your agent uses when identifying collaboration opportunities across fields, finding experts in complementary disciplines, translating methodologies between scientific domains, or building…

aipoch/medical-research-skills

A skill your agent uses when interpreting scientific graphs and charts, explaining data visualizations for research presentations, writing figure captions for publications, or analyzing trends in…

aipoch/medical-research-skills

Azure Fabric Management SDK for Python. An agent skill from microsoft/skills.

microsoft/skills

Azure Data Lake Storage Gen2 SDK for Python. An agent skill from microsoft/skills.

microsoft/skills

KQL language expertise for writing correct, efficient Kusto Query Language queries.

microsoft/skills

Launch, monitor, and manually clean up an eval job on Marin's Iris TPU or CoreWeave H100x8 GPU cluster via the OpenThoughts-Agent entrypoint.

open-thoughts/OpenThoughts-Agent

Follow the bundled R scatterplot specification. An agent skill from Jinze-Lee/codex-skills-workbench.

Jinze-Lee/codex-skills-workbench

A skill your agent uses when one validated cohort analysis must be repeated across many exposure/outcome pairs.

Aperivue/medsci-skills

A skill your agent uses when building batch jobs, ETL pipelines, scheduled imports/exports, or any chunk-oriented bulk processing with Spring Batch.

rrezartprebreza/spring-boot-skills

A skill your agent uses when building batch jobs, ETL pipelines, scheduled imports/exports, or any chunk-oriented bulk processing with Spring Batch.

rrezartprebreza/spring-boot-skills

Guideline-driven spatial analysis skill. An agent skill from GRIND-Lab-Core/night_owl_research_agent.

GRIND-Lab-Core/night_owl_research_agent

Process many sequence files in batch (count, merge, split, convert, summarize) with memory-safe streaming and on-disk indexing using Biopython, pysam, or pyfastx.

GPTomics/bioSkills

Creates DE-specific diagnostic and result visualizations using DESeq2/edgeR built-in functions and lightweight ggplot2 wrappers.

GPTomics/bioSkills

Defines cell populations in flow and spectral cytometry through manual gates (rectangle, polygon, quadrant, boolean) and reproducible automated gating (openCyto gating templates, flowDensity…

GPTomics/bioSkills

Handles BED-format genomic intervals (BED3 through BED12, narrowPeak/broadPeak) and the coordinate-system substrate the whole interval category rests on, with bedtools (CLI) and…

GPTomics/bioSkills

Parses, queries, converts, and extracts from GTF and GFF3 gene-model annotation files - walking the gene/transcript/exon/CDS hierarchy with gffutils (queryable SQLite DB), converting formats and…

GPTomics/bioSkills

Turns Hi-C/Micro-C FASTQ into a deduplicated, filtered .pairs file with pairtools and decides whether the library worked.

GPTomics/bioSkills

Renders Hi-C contact matrices honestly and reproducibly with matplotlib, cooltools, HiCExplorer, pyGenomeTracks, FAN-C, CoolBox, and plotgardener.

GPTomics/bioSkills

Load and preprocess imaging mass cytometry (IMC) and MIBI data from raw MCD/TXT through hot-pixel removal, spillover compensation, and variance-stabilizing transformation, covering readimc/steinbock…

GPTomics/bioSkills

Compare cell-type composition and spatial features across conditions in IMC/MIBI cohorts with the patient as the experimental unit, covering pseudoreplication, per-patient aggregation, mixed models…

GPTomics/bioSkills

Analyze spatial cell-cell interactions, neighborhoods, and niches in IMC/MIBI data with squidpy and imcRtools, covering neighborhood-enrichment permutation nulls, the abundance-vs-density confound…

GPTomics/bioSkills

Tracks ctDNA across serial liquid-biopsy timepoints for molecular residual disease (MRD) and treatment-response monitoring, treating MRD as a binary integrated detection call across the patient's…

GPTomics/bioSkills

Maps query single-cell data onto reference atlases and transfers cell-type labels using scArches surgery (scVI/scANVI), Symphony, Azimuth, CellTypist, scPoli, popV, and foundation models, with…

GPTomics/bioSkills

Selects biomarker features from high-dimensional omics data using Boruta all-relevant selection, mRMR, LASSO/elastic-net, and stability selection, while controlling the leakage, irreproducibility…

GPTomics/bioSkills

Validates predictive models on omics and biomedical data with nested cross-validation, group/batch/temporal-aware splits, the full data-leakage taxonomy, probability calibration, decision-curve net…

GPTomics/bioSkills

Builds diagnostic and prognostic classifiers on omics feature matrices with regularized logistic regression, random forest, and gradient-boosted trees, handling the pn regime, batch shortcut…

GPTomics/bioSkills

Explains ML predictions on omics data with SHAP, LIME, and permutation importance, handling the correlated-feature trap, the conditional-vs-interventional Shapley choice, and the…

GPTomics/bioSkills

Builds and validates predictive time-to-event models on clinical and omics data with penalized Cox, random survival forests, gradient-boosted and deep survival models, and prediction-grade…

GPTomics/bioSkills

Designs and analyzes stable-isotope-resolved metabolomics (SIRM / isotope tracing / fluxomics) experiments that measure metabolic ACTIVITY via 13C/15N/2H tracers, distinct from steady-state pool…

GPTomics/bioSkills

Assigns honest lipid annotation levels, designs class-based internal-standard quantification, and runs lipid-aware differential and enrichment analysis with lipidr, guarding against…

GPTomics/bioSkills

Turns untargeted LC-MS/MS features (m/z, RT, MS/MS) into confidence-stratified metabolite annotations using spectral-library matching (matchms), in-silico tools (SIRIUS/CSI:FingerID, MetFrag) and…

GPTomics/bioSkills

Designs QC, corrects signal drift, removes batch effects, filters features, normalizes samples, and imputes missing values for untargeted LC-MS/GC-MS metabolomics, framing each step as a measurement…

GPTomics/bioSkills

Maps metabolomics results to biological pathways via over-representation (ORA), metabolite-set enrichment (MSEA/QEA), mummichog/PSEA on raw m/z peaks, and network-diffusion enrichment (FELLA), with…

GPTomics/bioSkills

Decision-grade statistical analysis for metabolomics intensity tables.

GPTomics/bioSkills

Designs and validates quantitative targeted metabolomics assays (MRM/SRM on triple-quadrupole, PRM on high-resolution instruments) to report absolute concentrations.

GPTomics/bioSkills

Programmatic untargeted LC-MS feature extraction in R with the modern xcms 4.x MsExperiment/XcmsExperiment API, taking raw mzML to a feature table via CentWave peak detection, retention-time…

GPTomics/bioSkills

Turns a shotgun profiler table (MetaPhlAn relative abundance, Bracken counts, HUMAnN function tables) into honest figures and defensible community statistics with phyloseq, vegan, microViz, and…

GPTomics/bioSkills

Computes DNA methylation age (DNAm age) and pace of aging by applying frozen elastic-net epigenetic clocks to a clean beta matrix with methylclock, dnaMethyAge, or methylCIPHER.

GPTomics/bioSkills

Builds supervised and unsupervised multivariate integration across bulk omics blocks with mixOmics - sPLS for sparse pairwise correlation, DIABLO (block.splsda) for a multi-block discriminant…

GPTomics/bioSkills

Tests a ranked gene vector for coordinated expression shifts in GO, KEGG, Reactome, or MSigDB gene sets with clusterProfiler's gseGO, gseKEGG, gsePathway, and GSEA (fgseaMultilevel engine), and…

GPTomics/bioSkills

Draw and export phylogenetic trees with Bio.Phylo plus matplotlib, and route rich figures to ggtree, ETE4, or iTOL.

GPTomics/bioSkills

Computes linkage disequilibrium (r2, D', composite Rogers-Huff r2), prunes correlated variants, clumps GWAS summary statistics to lead SNPs, and defines haplotype blocks with PLINK 1.9/2.0 and…

GPTomics/bioSkills

In-memory Python population genetics with scikit-allel - GenotypeArray/HaplotypeArray/AlleleCountsArray, diversity (pi, theta, Tajima's D), SFS, FST (Weir-Cockerham, Hudson, Patterson), f3/D…

GPTomics/bioSkills

Builds and manages DIA spectral libraries as peptide query parameters (precursor m/z, a few fragment m/z plus relative intensities, normalized RT, optional CCS), covering experimental DDA…

GPTomics/bioSkills

Exports publication-ready figures with the correct vector/raster split, embedded editable fonts, color-space-robust palettes, and journal-correct sizing and resolution in matplotlib and ggplot2.

GPTomics/bioSkills