Data & Analytics · Bioinformatics

Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats.

spacering-net/codeg

Walks through single-cell RNA-seq analysis with Scanpy: loading .h5ad and 10X data, QC, normalization, PCA and UMAP, Leiden clustering, marker genes and cell type annotation.

davila7/claude-code-templates

Load when the user needs Deterministic fixed-period 24-hour single-component cosinor OLS rhythm analysis for a bulk RNA time-course CSV.

TianGzlab/OmicsClaw

Guides use of deepTools on sequencing data: BAM to bigWig conversion, QC, sample correlation, and heatmaps or profiles around TSS and peaks for ChIP-seq, RNA-seq and ATAC-seq.

davila7/claude-code-templates

Manages biological datasets with LaminDB: versioned artifacts, run lineage, ontology-based annotation, schema validation and links to workflow managers and ML tools.

davila7/claude-code-templates

200以上のファイル形式に対応した探索的データ分析（EDA）スキル. An agent skill from minicoohei/ai-agent-camp.

minicoohei/ai-agent-camp

Runs differential gene expression analysis on bulk RNA-seq counts with PyDESeq2: design formulas, Wald tests, FDR correction and volcano or MA plots.

davila7/claude-code-templates

Works with genomic intervals using gtars, a Rust toolkit with Python bindings: overlap detection, coverage tracks, tokenization for ML models and reference sequences.

davila7/claude-code-templates

Computational pathology toolkit for analyzing whole-slide images (WSI) and multiparametric imaging data.

davila7/claude-code-templates

Python interface to OpenMS for mass spectrometry data analysis.

davila7/claude-code-templates

Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats.

aipoch/medical-research-skills

Runs a seven-step quality-control and exploration pipeline on scRNA-seq, CyTOF or flow cytometry data and writes a plain-language report of what it found.

LigphiDonk/Oh-my--paper

Turns raw flux balance analysis output and a COBRApy model into gene essentiality maps, phenotypic phase planes, flux sampling results, pathway summaries and secretion predictions.

aiming-lab/AutoResearchClaw

Load when correcting batch effects in bulk expression using R sva ComBat or the legacy Python parametric approximation.

TianGzlab/OmicsClaw

Query NHGRI-EBI GWAS Catalog for SNP-trait associations. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

Load when discovering bulk gene co-expression modules and hub genes with R WGCNA.

TianGzlab/OmicsClaw

Fetch a regional slice of plasma pQTL summary statistics from the UK Biobank Pharma Proteomics Project (UKB-PPP; Sun 2023 Nature) for a specific (protein, ancestry) measurement.

ClawBio/ClawBio

Infers candidate gene regulatory networks from bulk or single-cell expression data using AertsLab Arboreto GRNBoost2 and GENIE3.

K-Dense-AI/scientific-agent-skills

Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics.

GPTomics/bioSkills

Fast genomic interval operations (overlap, nearest, merge, coverage, cluster, complement, subtract, count-overlaps), multi-format bioinformatics I/O, DataFusion SQL, and pileup on Polars DataFrames…

ClawBio/ClawBio

Performs genomic interval overlap, nearest, merge, coverage, complement and subtraction on Polars DataFrames, and reads or writes BED, VCF, BCF, BAM, CRAM, GFF, GTF, FASTA and FASTQ data.

K-Dense-AI/scientific-agent-skills

Load when converting Ensembl, Entrez or symbol IDs in a bulk RNA count matrix using an explicit mapping or a small human demo reference.

TianGzlab/OmicsClaw

Load when querying STRING for the protein-protein interaction neighborhood of a bulk RNA-seq DEG list and finding hub genes.

TianGzlab/OmicsClaw

End-to-end GWAS automation wrapping PLINK2 for genotype QC and REGENIE for two-step whole-genome regression association testing.

ClawBio/ClawBio

A skill your agent uses when creating, migrating, or debugging pixi environments, especially for scientific Python, bioinformatics, single-cell analysis, CUDA/PyTorch, Jupyter/VS Code kernels…

xuzhougeng/wisp-science

Build and interpret polygenic risk scores (PRS) for complex diseases using GWAS summary statistics.

wu-yc/LabClaw

Load when checking a bulk RNA-seq count matrix for library-size outliers, gene detection rates, and sample-sample correlation before DE.

TianGzlab/OmicsClaw

In recent years a wealth of biological data has become available in public data repositories.

bioMate-AI/biomate-bioconductor-kb

Generate R/Python code for volcano plots from DEG (Differentially Expressed Genes) analysis results.

aipoch/medical-research-skills

Visualize copy number profiles, segments, allele-specific tracks, and cohort patterns from CNVkit, GATK, ASCAT, FACETS, Sequenza, and other callers.

GPTomics/bioSkills

Identifies essential genes from CRISPR-Cas9 fitness screens using BAGEL2 (Kim & Hart 2021 Genome Med), a Bayesian classifier scoring per-gene Bayes Factors via log-likelihood ratios over per-sgRNA…

GPTomics/bioSkills

Build circular genome visualizations using circlize (R), pyCirclize (Python), or Circos (Perl CLI) with ideogram tracks, multi-data tracks (scatter, histogram, heatmap), chord/link arcs for…

GPTomics/bioSkills

Produce and interpret PCA, t-SNE, UMAP, and PHATE plots for high-dimensional omics data with rigor about which method preserves what (variance, local structure, manifold, transitions)…

GPTomics/bioSkills

Build genome-browser-style multi-track figures with pyGenomeTracks (config-driven), Gviz (R), and IGV batch screenshotting.

GPTomics/bioSkills

Build Manhattan, Miami, QQ, and locuszoom-style regional plots from GWAS, TWAS, PWAS, and QTL summary statistics with correct genomic-inflation diagnostics, multi-trait overlays, lead-SNP labeling…

GPTomics/bioSkills

Detects aberrant splicing in single rare-disease patients vs a control panel using FRASER 2.0 (Bioconductor; Beta-binomial autoencoder on Intron Jaccard Index, default delta cutoff 0.1, q…

GPTomics/bioSkills

Creates sashimi-style plots showing RNA-seq read coverage and splice junction counts using ggsashimi (general-purpose, condition-grouped overlays), rmats2sashimiplot (rMATS-output-aware)…

GPTomics/bioSkills

Production-ready genomics and epigenomics data processing for BixBench questions.

wu-yc/LabClaw

Analyze metabolomics data including metabolite identification, quantification, pathway analysis, and metabolic flux.

wu-yc/LabClaw

Load when summarising STAR / HISAT2 / Salmon alignment-rate logs in bulk RNA-seq.

TianGzlab/OmicsClaw

Process multiple sequence files in batch using Biopython. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.

FreedomIntelligence/OpenClaw-Medical-Skills

Visualize Hi-C contact matrices, TADs, loops, and genomic features using matplotlib, cooltools, and HiCExplorer.

FreedomIntelligence/OpenClaw-Medical-Skills

Cell segmentation from multiplexed tissue images. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.

FreedomIntelligence/OpenClaw-Medical-Skills

Visualize metagenomic profiles using R (phyloseq, microbiome) and Python (matplotlib, seaborn).

FreedomIntelligence/OpenClaw-Medical-Skills

Load and parse mass spectrometry data formats including mzML, mzXML, and quantification tool outputs like MaxQuant proteinGroups.txt.

FreedomIntelligence/OpenClaw-Medical-Skills

Analyze time-series RNA-seq data using limma voom with splines, maSigPro, and ImpulseDE2.

FreedomIntelligence/OpenClaw-Medical-Skills

Cell type assignment from marker expression in IMC data. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.

FreedomIntelligence/OpenClaw-Medical-Skills

Quality control and assessment for proteomics data. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.

FreedomIntelligence/OpenClaw-Medical-Skills