MCP App StoreMCP App Store
End-to-end pipeline for short-read bulk RNA-seq alternative splicing analysis: QC, STAR 2-pass alignment, junction QC, rMATS differential splicing, isoform swit
Provides a complete workflow to analyze alternative splicing from raw FASTQ to differential splicing results in bulk short-read RNA-seq experiments. The skill documents steps for QC (fastp), STAR 2-pass alignment, junction quality control, differential splicing with rMATS-turbo, optional isoform-switching analyses (IsoformSwitchAnalyzeR), and sashimi plot generation for visualization.
Use when you have cohort-style short-read RNA-seq data and need to detect differential splicing between two groups, perform QC on junction detection, or generate publication-ready visualizations of splicing events. Not suitable for single-sample rare-disease outlier detection, splice-variant prediction workflows, or long-read full-isoform analysis.
Agents that can orchestrate long-running bioinformatics workflows or output shell commands and scripts (e.g., agents with shell/cluster submission support, or that can generate reproducible pipelines).
Documentation-only skill for bulk RNA-seq alternative splicing analysis (STAR 2-pass + rMATS-turbo + IsoformSwitchAnalyzeR). No bundled scripts. SKILL.md is thorough with clear pipeline steps, variant routing table, and code examples. Minor code quality issues like inline __import__('numpy') and truncated complete pipeline script. Niche bioinformatics audience with heavy dependency requirements.
Clean reference skill with no security concerns. Good domain coverage with clear routing to related skills for different analysis regimes. Architecture could improve by separating code examples into scripts/ directory.
arXiv Search
Search arXiv for recent preprints and build local Markdown summaries; ideal for CS, math, physics, and quantitative-bio literature discovery.
PLINK Basics
Commands and examples for converting genotype formats and running standard QC filters (MAF, geno, mind, HWE) with PLINK 1.9/2.0.
AlphaFold Structure Query
Query the AlphaFold EBI API to fetch predicted protein structures, download PDB/CIF files, and inspect confidence metrics (pLDDT/PAE).
PyTorch Geometric (PyG) Guide
Authoritative guide for building and scaling Graph Neural Networks using PyTorch Geometric: data, layers, training patterns, and common pitfalls.
DnaSP (ClawBio)
Run DnaSP-style population genetics analyses (π, Tajima's D, LD, MK, Ka/Ks, SFS) on aligned sequences locally and produce TSV/Markdown reports.
Seq Wrangler
Sequence data QC, trimming, alignment, and BAM processing pipeline helper — wraps FastQC, fastp/Trimmomatic, BWA/Bowtie2/Minimap2, and SAMtools for automated re
Scientific Schematics & Diagrams
Generate publication-quality scientific diagrams via AI with iterative quality review and smart regeneration for journal, conference, poster, and presentation o
Retriever (Membrane) Integration
Integrate with Retriever via the Membrane CLI to search, query, and proxy Retriever data (documents, snippets, queries) with built-in auth and pagination.
Plotly (Interactive Python Visualizations)
Interactive Python visualization skill for building hoverable, zoomable, and embeddable charts (Plotly Express + Graph Objects) for EDA, dashboards, and present
Manim Idea to Export
Turn plain-language concepts into production-ready ManimCE scene blueprints, runnable code, preview renders, and final export commands for video assets.
PPT as Code
Creator-first workflow to plan and build HTML-first presentations with staged modes (quick/basic/advanced), optional PPTX export, and clear QA and image plannin
ToolUniverse Gateway
Unified agent gateway to 1000+ scientific tools (bioinformatics, drug discovery, genomics) via Harvard's ToolUniverse, returning JSON for downstream workflows.
Crucible: Build
Orchestrates an end-to-end development pipeline: interactive design, planning, autonomous execution, and quality gates with TDD and iterative reviews.