stanfish06/skillquarium - Page 3

archaic-introgression

Detect Neanderthal and Denisovan introgression segments from modern human genomes

Langue du texte source : anglais

caveman-compress

Compress a memory file such as CLAUDE.md or a todo list into caveman format to save input tokens, keeping a readable backup. Trigger: /caveman-compress.

Langue du texte source : anglais

hla-typing

HLA allele typing from WGS/WES VCF data

Langue du texte source : anglais

proteomics-de

Differential expression analysis for label-free quantitative (LFQ) intensity data with standard MaxQuant and DIA-NN output. Workflow includes preprocessing, imputation, and statistical testing.

Langue du texte source : anglais

great-expectations

Data validation using Great Expectations. Expectation suites, checkpoints, and data docs for pipeline monitoring.

Langue du texte source : anglais

claw-ancestry-pca

Ancestry decomposition PCA against the Simons Genome Diversity Project

Langue du texte source : anglais

fitness-nutrition

Gym workout planner and nutrition tracker. Search 690+ exercises by muscle, equipment, or category via wger. Look up macros and calories for 380,000+ foods via USDA FoodData Central. Compute BMI, TDEE, one-rep max, macro splits, and body fat — pure Python, no…

Langue du texte source : anglais

ld-1000g-region-compute

Compute pairwise r² between a lead variant and every variant in a window using the 1000 Genomes Phase 3 GRCh38 reference panel, ancestry-stratified. Use when an agent needs LD coloring for a regional plot or LD pruning around a candidate causal variant.…

Langue du texte source : anglais

pydicom

Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when reading, writing, or modifying medical imaging data in DICOM format, extracting pixel data from medical images (CT, MRI, X-ray, ultrasound),…

Langue du texte source : anglais

deep-research

Universal deep research agent team. 13-agent pipeline for rigorous academic research on any topic. 8 modes: full research, quick brief, paper review, lit-review, fact-check, three-way literature scan, Socratic guided research dialogue, and systematic review…

Langue du texte source : anglais

dnanexus-integration

DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.

Langue du texte source : anglais

paper-2-web

Use when converting academic papers into promotional and presentation formats including interactive websites (Paper2Web), presentation videos (Paper2Video), and conference posters (Paper2Poster). Use this skill for tasks involving paper dissemination,…

Langue du texte source : anglais

c-review

Performs comprehensive C/C++ security review for memory corruption, integer overflows, race conditions, and platform-specific vulnerabilities. Use when auditing native C/C++ applications, reviewing daemons or services for memory safety, or hunting integer…

Langue du texte source : anglais

constant-time-analysis

Detects timing side-channel vulnerabilities in cryptographic code. Use when implementing or reviewing crypto code, encountering division on secrets, secret-dependent branches, or constant-time programming questions in C, C++, Go, Rust, Swift, Java, Kotlin,…

Langue du texte source : anglais

struct-predictor

Protein structure prediction with Boltz-2. Accepts YAML inputs (single protein or multi-chain complex), runs boltz predict, extracts per-residue pLDDT and PAE confidence, and writes a markdown report with figures.

Langue du texte source : anglais

lit-synthesizer

Search PubMed and bioRxiv for bioinformatics literature, synthesise results into a structured report, and build a citation graph — all locally, with a reproducibility bundle.

Langue du texte source : anglais

skills-hub

Browse and install community skills from the BioClaw Skills Hub. Use when a user's task is not covered by built-in skills, or when the user asks about available skills, advanced workflows, or specialized analysis pipelines. Triggers on "skills hub", "more…

Langue du texte source : anglais

ngs-amplicon-microbiome

Kick off public 16S, 18S, ITS, COI, or other marker-gene amplicon microbiome workflows using nf-core/ampliseq, QIIME2, DADA2, and Cutadapt.

Langue du texte source : anglais

ngs-analysis-router

Route BCL, FASTQ, BAM/CRAM, count-matrix, or VCF sequencing requests to the right public NGS analysis skill and ask only the missing assay-specific setup questions.

Langue du texte source : anglais

ngs-atacseq-peaks-qc

Run or plan ATAC-seq QC, alignment, TSS enrichment, fragment-size, blacklist, peak-calling, consensus peak, and differential accessibility workflows.

Langue du texte source : anglais

ngs-bcl-to-fastq

Validate Illumina BCL run folders and sample sheets, plan demultiplexing, review index/UMI/lane choices, run BCL-to-FASTQ conversion, and interpret demux metrics while surfacing license/download boundaries.

Langue du texte source : anglais

ngs-bulk-rnaseq-counts-qc

Run or plan bulk RNA-seq FASTQ-to-count processing with sample-sheet, strandedness, genome annotation, alignment or pseudoalignment, MultiQC, and count-matrix QC checks.

Langue du texte source : anglais

ngs-bulk-rnaseq-differential-expression

Run or plan bulk RNA-seq differential-expression analysis from count matrices with replicate, design formula, contrast, batch, normalization, QC plot, and result-table checks.

Langue du texte source : anglais

ngs-bulk-rnaseq

Dispatch bulk RNA-seq requests to FASTQ-to-count QC or count-matrix differential-expression skills using nf-core/rnaseq, STAR, Salmon, featureCounts, MultiQC, and R/Bioconductor workflows.

Langue du texte source : anglais

ngs-chip-cutrun-peaks-qc

Run or plan ChIP-seq, CUT&RUN, or CUT&Tag QC, control handling, spike-in, peak calling, broad-vs-narrow target selection, replicate, bigWig, and differential binding workflows.

Langue du texte source : anglais

ngs-dna-germline-variants

Run or plan deep germline WGS, WES, targeted-panel, cohort, or trio variant-calling workflows with reference-build, known-sites, QC, joint-calling, and annotation checks.

Langue du texte source : anglais

ngs-dna-somatic-variants

Run or plan tumor-normal, tumor-only, WGS, WES, or cancer-panel somatic variant workflows with pairing, contamination, panel-of-normals, purity, QC, and annotation checks.

Langue du texte source : anglais

ngs-dna-umi-panel-variants

Run or plan targeted DNA panel variant workflows that use UMIs, duplex consensus reads, molecular barcodes, low-frequency calling, target coverage, and panel-specific QC.

Langue du texte source : anglais

ngs-dna-variant-calling

Dispatch WGS, WES, or targeted DNA variant requests to germline, somatic, or UMI-panel skills, then plan public nf-core/sarek, GATK4, DeepVariant, samtools, or bcftools workflows.

Langue du texte source : anglais

ngs-epigenomics-peaks

Dispatch ATAC-seq, ChIP-seq, CUT&RUN, or CUT&Tag requests to assay-specific QC, alignment, signal-track, peak-calling, consensus, and differential peak workflows.

Langue du texte source : anglais

ngs-fastq-qc

Validate FASTQ inputs, run local FastQC/MultiQC QC, interpret QC signals, and optionally execute fastp or Cutadapt trimming branches without overwriting raw reads.

Langue du texte source : anglais

ngs-runtime-env

Check whether public NGS tools and packages already exist before downloading, installing, or running a sequencing pipeline.

Langue du texte source : anglais

ngs-scrna-seq

Route single-cell or single-nucleus RNA-seq FASTQs to public count-generation workflows and defer post-count matrix QC, annotation, clustering, and UMAP analysis to the embedded scrna-seq-qc skill.

Langue du texte source : anglais

ngs-shotgun-metagenomics

Kick off public shotgun metagenomics QC, host-depletion, taxonomic profiling, and functional profiling workflows using nf-core/taxprofiler, Kraken2, Bracken, MetaPhlAn, and HUMAnN.

Langue du texte source : anglais

scrna-seq-qc

Process, quality-control, annotate, and visualize single-cell or single-nucleus RNA-seq datasets across tissues and species. Use when Codex needs to build, adapt, or review a general scRNA-seq QC pipeline; choose dataset-appropriate cell-level filters from QC…

Langue du texte source : anglais

building-ai-agent-on-cloudflare

Builds AI agents on Cloudflare using the Agents SDK with state management, real-time WebSockets, scheduled tasks, tool integration, and chat capabilities. Generates production-ready agent code deployed to Workers. Use when: user wants to "build an agent", "AI…

Langue du texte source : anglais

gwas-prs

Calculate polygenic risk scores from DTC genetic data using the PGS Catalog

Langue du texte source : anglais

officecli-word-form

Use this skill to create fillable Word forms (.docx) with real Content Controls (SDT) + legacy FormField checkboxes + MERGEFIELD mail-merge placeholders + document protection. Trigger on: 'fillable form', 'form fields', 'content controls', 'SDT', 'word form',…

Langue du texte source : anglais

fetching-dbt-docs

Retrieves and searches dbt documentation pages in LLM-friendly markdown format. Use when fetching dbt documentation, looking up dbt features, or answering questions about dbt Cloud, dbt Core, or the dbt Semantic Layer.

Langue du texte source : anglais

complexa-design

End-to-end Proteina-Complexa design pipeline driver. Use when the user wants to "design a binder", "design binders for X", "run complexa design", "de novo binder", "PDL1 binder", "TrkA binder", "design proteins for target", "protein binder design", "ligand…

Langue du texte source : anglais