Microbiologists

Scvelo

RNA velocity analysis with scVelo. Estimate cell state transitions from unspliced/spliced mRNA dynamics, infer trajectory directions, compute latent time, and identify driver genes in single-cell RNA-seq data. Complements Scanpy/scVI-tools for trajectory inference.

lamm-mit179

Structural Variant Analysis

ToolUniverse workflow — Structural Variant Analysis

lamm-mit179

Deeptools

NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.

Microck172

Vuln Research

安全研究元思考方法论 - 从先知社区5600+篇安全文档中提炼的漏洞挖掘方法论框架。 Use this skill when: - 进行漏洞挖掘和安全研究时，需要系统化的思考框架 - 分析特定类型漏洞（Web注入、反序列化、二进制、域渗透等）的攻击路径 - 需要了解绕过防护措施（WAF、EDR、沙箱）的思维模式 - 进行代码审计需要Source-Sink分析方法论 - 红队攻防需要完整攻击链规划 - CTF竞赛需要快速解题思路 - 逆向分析恶意软件需要方法论指导 Triggers: 漏洞挖掘、安全研究、渗透测试、代码审计、红队攻防、CTF、逆向分析、 WAF绕过、免杀、提权、横向移动、域渗透、反序列化、二进制安全、Fuzzing

tanweai159

Variant Clinical Significance

Query NCBI ClinVar for variant clinical pathogenicity classification (Pathogenic/Benign/VUS), review status and associated diseases.

Dokumente

Lab Protocol From Literature

Lab Protocol from Literature - Extract and generate lab protocol: search PubMed, extract protocol from paper, and generate executable protocol. Use this skill for lab science tasks involving pubmed search extract protocol from pdf protocol generation generate executable json. Combines 4 tools from 2 SCP server(s).

Variant Cross Database Ids

Query ClinGen Allele Registry to map variant rsID to identifiers in other databases (ClinVar, gnomAD, COSMIC, UniProtKB, OMIM, etc.).

One Health Analysis

One Health Pathogen Analysis - One Health analysis: pathogen genome, cross-species gene comparison, antimicrobial drugs, and environmental context. Use this skill for one health tasks involving get genome dataset report by taxon get homology symbol get mechanism of action by drug name tavily search get taxonomy. Combines 5 tools from 4 SCP server(s).

Datenanalyse

Volcano Plot Labeler

Analyze data with `volcano-plot-labeler` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.

Datenanalyse

Metagenomic Krona Chart

Analyze data with `metagenomic-krona-chart` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.

Dokumente

Flowio

Parse Flow Cytometry Standard (FCS) files v2.0–3.1 and extract events/metadata for preprocessing workflows (e.g., when you need NumPy arrays, channel info, or CSV/DataFrame export from cytometry files).

Datenanalyse

Meta Baujat Plot

Generate Baujat plots for heterogeneity analysis. Identify studies that contribute most to the overall meta-analysis results and heterogeneity, helping discover potential outlier studies. Input meta-analysis data CSV, output Baujat plot PNG and contribution data CSV.

Adme Property Predictor

Analyze data with `adme-property-predictor` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.

Microbiome Diversity Reporter

Interpret Alpha and Beta diversity metrics from 16S rRNA sequencing results.

Dokumente

Fastqc Report Interpreter

Use when analyzing FASTQC quality reports from sequencing data, identifying quality issues in NGS datasets, or troubleshooting sequencing problems. Interprets quality metrics and provides actionable recommendations for RNA-seq, DNA-seq, and ChIP-seq data.

One Health Analysis

Structural Pharmacogenomics

Structural Pharmacogenomics - Link structure to pharmacogenomics: variant effect, protein structure change, drug binding, and clinical data. Use this skill for pharmacogenomics tasks involving get vep hgvs pred protein structure esmfold boltz binding affinity get pharmacogenomics info by drug name. Combines 4 tools from 3 SCP server(s).

Boltz2 Binding Affinity

Predict protein-ligand binding affinity using Boltz-2 model to assess molecular interactions and binding probability for drug discovery.

Wissenschaftliches Rechnen

Virus Genomics

Virus Genomics Analysis - Analyze virus genomics: NCBI virus dataset, annotation, taxonomy, and literature search. Use this skill for virology tasks involving get virus dataset report get virus annotation report get taxonomy search literature. Combines 4 tools from 2 SCP server(s).

Metabolomics Quantification

Feature quantification, missing value imputation, and normalization for metabolomics data.

Proteomics Quantification

Protein/peptide quantification (LFQ, TMT, DIA) using MaxQuant LFQ, DIA-NN, or Skyline.

Proteomics De

Differential protein abundance testing using MSstats, limma, proDA, and scipy/statsmodels for Python. Multiple testing correction with BH FDR.

Metabolomics Annotation

Metabolite annotation and structural identification using SIRIUS, CSI:FingerID, GNPS, or MetFrag.

Bulkrna Read Qc

FASTQ quality assessment for bulk RNA-seq — Phred scores, GC content, adapter detection, read length distribution, Q20/Q30 rates.

Salmon — Fast RNA-seq Quantification

Ultra-fast RNA-seq transcript and gene-level quantification using quasi-mapping (no BAM required). Builds a k-mer index from a transcriptome FASTA, then quantifies reads in minutes. Outputs transcript-level TPM/count tables (quant.sf) with optional GC-bias and sequence-bias correction. Integrates directly with tximeta/tximport for DESeq2 or edgeR. Use STAR instead when a genome-aligned BAM is required for variant calling or visualization.

trackpy

Python library for tracking particles (fluorescent spots, colloids, vesicles, cells) in video microscopy using the Crocker-Grier algorithm. Core modules: locate particles in single frames, batch-process image sequences, link positions into trajectories, filter short-lived tracks, and compute mean squared displacement (MSD) for diffusion analysis. Supports 2D and 3D tracking with subpixel accuracy. Integrates with pims for reading TIF stacks, AVI, and image series. Use when you need quantitative single-particle tracking (SPT) from fluorescence or brightfield video and downstream diffusion coefficient extraction.

SimpleITK Image Registration and Analysis

Register, segment, filter, and resample 3D medical images (MRI, CT, microscopy) using SimpleITK's Python API with support for DICOM, NIfTI, and multi-modal image analysis. Provides rigid/affine/deformable registration, threshold and region-growing segmentation, Gaussian and morphological filtering, label statistics, and format conversion. Use when aligning volumetric images across timepoints or modalities, automating segmentation of fluorescence microscopy, or converting DICOM series to NIfTI for analysis pipelines.

PRIDE Database

Search and retrieve proteomics datasets, peptide identifications, and mass spectrometry raw data files from the PRIDE Archive REST API. Find experiments by organism, tissue, disease, or instrument; download RAW/mzML files; retrieve peptide and PSM identifications; access protein-level evidence. For protein domain architecture use interpro-database; for protein sequences and annotations use uniprot-protein-database.

Wissenschaftliches Rechnen

Cellpose — Deep Learning Cell Segmentation

Deep learning cell and nucleus segmentation from fluorescence and brightfield microscopy images. Uses pre-trained models (cyto3, nuclei, tissuenet) and a generalist flow-based algorithm that segments cells without requiring retraining on new image types. Outputs label masks for downstream morphology measurement and tracking. Use scikit-image watershed for rule-based segmentation; use Cellpose when deep learning generalization across staining conditions is needed.