Detect positive (diversifying / episodic / pervasive) selection using codon dN/dS frameworks. Implements PAML codeml site models (M0/M1a/M2a/M7/M8/M8a), branch models, branch-site…
When the user wants to write, publish, republish, or optimize posts on Medium.com (canonical tags, distribution, Medium SEO).
When the user wants to create Pinterest Pins, optimize Pin descriptions, or grow Pinterest presence. Also use when the user mentions "Pinterest," "Pin," "Pinterest SEO," — from…
Test whether two traits share a causal variant at a genomic locus using Bayesian colocalization with coloc.
Execute autonomous multi-step research using Google Gemini Deep Research Agent. Use for: market analysis, competitive landscaping, literature reviews, technical research — from…
Searches for non-coding RNA homologs and classifies RNA families using Infernal covariance model searches against the Rfam database.
Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational mate — from…
Manual and automated gating for defining cell populations in flow cytometry. Covers rectangular, polygon, and data-driven gates.
Build Retrieval-Augmented Generation (RAG) systems for LLM applications with vector databases and semantic search.
Complete mass spectrometry analysis platform. Use for proteomics workflows feature detection, peptide identification, protein quantification, and complex LC-MS/MS pipelin — from…
When the user wants to create LinkedIn post copy or optimize for LinkedIn. Also use when the user mentions "LinkedIn post," "LinkedIn article," "professional post," "post — from…
Reads, queries, and writes bigWig indexed binary signal tracks (coverage, fold-change, conservation, methylation-rate) with pyBigWig (Python) and the UCSC Kent tools…
Designs pegRNAs and nicking guides for prime editing (PE) -- choosing the nick/strand, tuning the primer-binding site (PBS) and reverse-transcription template (RTT) as a per-locus…
Conduct comprehensive deep research on any topic using Dify-powered workflow - searches documentation, academic papers, tutorials, APIs, best practices, and returns structured…
Detects m6A modifications from Oxford Nanopore direct-RNA-sequencing (ONT DRS) signal data using m6Anet (Hendra 2022 *Nat Methods* 19:1590; multiple-instance-learning neural…
Presentation toolkit (.pptx). Create/edit slides, layouts, content, speaker notes, comments, for programmatic presentation creation and modification.
Installs 425 bioinformatics skills covering sequence analysis, RNA-seq, single-cell, variant calling, metagenomics, structural biology, and 56 more categories.
Quantify transcript expression using pseudo-alignment with Salmon or kallisto. Use when quantifying transcripts with Salmon or kallisto. — from bg-szy/TOP-SKILLS
When the user wants to define, audit, or apply visual identity (typography, colors, spacing, design tokens, frontend aesthetics).
Clean Architecture and SOLID principles guide. Use this when designing systems, reviewing architecture, or making structural decisions.
Preprocess CLIP-seq reads (eCLIP, iCLIP, iCLIP2, iCLIP3, irCLIP, PAR-CLIP, FLASH) with protocol-specific UMI extraction, adapter trimming, length filtering, and post-alignment…
Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem.
Spawn a new terminal window to run CLI commands (ffmpeg, curl, python, etc.). Use for non-AI command execution. — from bg-szy/TOP-SKILLS
Query Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target — from…
Infer cis-regulatory connections (peak-to-peak co-accessibility) from scATAC-seq using Cicero, ArchR getCoAccessibility, or SCENIC+.
Infer integer allele-specific copy number, tumor purity, and ploidy from tumor sequencing by jointly modeling read depth (logR) and B-allele frequency (BAF) with ASCAT, Sequenza,…
Orchestrates an end-to-end MeRIP-seq / m6A-seq analysis from raw FASTQ to differential m6A peak calls and metagene plots, chaining fastp adapter trimming, STAR splice-aware genome…
Bead-based normalization for CyTOF and high-parameter flow cytometry. Covers EQ bead normalization, signal drift correction, and batch normalization.
Implement efficient similarity search with vector databases. Use when building semantic search, implementing nearest neighbor queries, or optimizing retrieval performance — from…
Designs and analyzes combinatorial CRISPR screens covering paired-Cas9 (Big Papi, Najm 2018), enhanced AsCas12a multiplex (enCas12a, DeWeirdt 2021), in4mer 4-guide-array Cas12a…
Analyze drug safety signals from FDA adverse event reports, label warnings, and pharmacogenomic data.
Automate GitHub workflows with AI assistance. Includes PR reviews, issue triage, CI/CD integration, and Git operations.
Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data m — from…
Comprehensive document creation, editing, and analysis with support for tracked changes, comments, formatting preservation, and text extraction.
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similar — from…
When the user wants to optimize URL structure, fix URL issues, or plan URL hierarchy. Also use when the user mentions "URL structure," "URL optimization," "slug," "clean URLs,"…
Detect signatures of natural selection using Fst, Tajima's D, iHS, XP-EHH, and other selection statistics.
Automate Twitter/X with posting, engagement, and user management via inference.sh CLI. Apps: x/post-tweet, x/post-create (with media), x/post-like, x/post-retweet, x/dm-s — from…
Peptide-spectrum matching and protein identification from MS/MS data. Use when identifying peptides from tandem mass spectra.
Call accessible chromatin regions from ATAC-seq BAM files using MACS3, MACS2, Genrich, or HMMRATAC. Use when identifying open chromatin from aligned ATAC-seq, choosing between…
Create commit messages following Sentry conventions. Use when committing code changes, writing commit messages, or formatting git history.
Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for — from…
Perform differential expression analysis using DESeq2 in R/Bioconductor. Use for analyzing RNA-seq count data, creating DESeqDataSet objects, running the DESeq workflow, and…
Generate images with Alibaba Qwen-Image-2.0-Pro via inference.sh CLI. Professional text rendering, fine-grained realism, enhanced semantic adherence.
Data-independent acquisition (DIA) proteomics analysis with DIA-NN and other tools. Use when analyzing DIA mass spectrometry data with library-free or library-based workf — from…
Per-CpG differential methylation testing from bisulfite sequencing count data or beta-value matrices.
When the user wants to design, optimize, or audit grid layouts for content display. Also use when the user mentions "grid layout," "grid design," "multi-column grid," "CSS grid,"…
Design guides for cytosine and adenine base editing using editing window optimization and BE-Hive outcome prediction.
Analyze single-cell TCR and BCR data integrated with gene expression using scirpy. Use when working with 10x Genomics VDJ data alongside scRNA-seq or when integrating imm — from…
Build reproducible scientific documents, presentations, and websites with Quarto supporting R, Python, Julia, and Observable JS.
Fits structural equation models to GWAS summary statistics using GenomicSEM (Grotzinger 2019), including common-factor models, confirmatory factor models, ESEM, common-fa — from…
Assesses ChIP-seq quality across antibody specificity, fragmentation, enrichment, replicate concordance, and library complexity.
Computational analysis framework for spatial multi-omics data integration. Given spatially variable genes (SVGs), spatial domain annotations, tissue type, and disease con — from…
Transforms workflow to use Manus-style persistent markdown files for planning, progress tracking, and knowledge storage.
Create and manage Claude Code skills with auto-activation, progressive disclosure, and memory patterns.
When the user wants to add, optimize, or design customer testimonials, reviews, or case study sections.
Quick project setup with templates, best practices, and complete configuration for various framew...
Discover novel miRNAs and quantify known miRNAs using miRDeep2 de novo prediction from small RNA-seq data.
Taxonomic classification of ASVs using reference databases like SILVA, GTDB, or UNITE. Covers naive Bayes classifiers (DADA2, IDTAXA) and exact matching approaches.
Clinical variant interpretation using ClinVar, ACMG guidelines, and pathogenicity predictors. Prioritize variants for diagnostic and research applications.