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Extract nucleosome positions from ATAC-seq data using NucleoATAC, ATACseqQC, and fragment analysis. Use when analyzing chromatin organization, identifying nucleosome-free regions at promoters, or characterizing nucleosome occupancy patterns from ATAC...
End-to-end ChIP-seq workflow from FASTQ files to annotated peaks. Covers QC, alignment, peak calling with MACS3, and peak annotation with ChIPseeker. Use when processing ChIP-seq data from alignment through peak annotation.
End-to-end 16S amplicon workflow from FASTQ reads to differential abundance. Orchestrates DADA2 ASV inference, taxonomy assignment, diversity analysis, and compositional testing with ALDEx2. Use when processing 16S/ITS amplicon data.
Quality control, filtering, and normalization for single-cell RNA-seq using Seurat (R) and Scanpy (Python). Use for calculating QC metrics, filtering cells and genes, normalizing counts, identifying highly variable genes, and scaling data. Use when f...
Visualize Hi-C contact matrices, TADs, loops, and genomic features using matplotlib, cooltools, and HiCExplorer. Create triangle plots, virtual 4C, and multi-track figures. Use when visualizing contact matrices or genomic features.
End-to-end CRISPR screen analysis from FASTQ to hit genes. Orchestrates guide counting, QC, statistical analysis with MAGeCK, and hit calling with multiple methods. Use when analyzing pooled CRISPR screens from count data to hit calling.
Extract, filter, annotate, and export differential expression results from DESeq2 or edgeR. Use for identifying significant genes, applying multiple testing corrections, adding gene annotations, and preparing results for downstream analysis. Use when...
Design guides for cytosine and adenine base editing using editing window optimization and BE-Hive outcome prediction. Select optimal positions for C-to-T or A-to-G conversions without double-strand breaks. Use when designing base editor experiments f...
Cell-free DNA analysis pipeline from plasma sequencing to tumor monitoring. Preprocesses cfDNA reads, analyzes fragment patterns, estimates tumor fraction from sWGS, and optionally detects mutations from targeted panels. Use when analyzing liquid bio...
End-to-end copy number variant detection workflow from BAM files. Covers CNVkit analysis for exome/targeted sequencing with visualization and annotation. Use when detecting copy number alterations from sequencing data.
MS-DIAL-based metabolomics preprocessing as alternative to XCMS. Covers peak detection, alignment, annotation, and export for downstream analysis. Use when processing MS-DIAL output files for R/Python analysis or when preferring GUI-based preprocessi...
Analyze time-series RNA-seq data using limma voom with splines, maSigPro, and ImpulseDE2. Identify genes with dynamic expression patterns. Use when analyzing time-series or longitudinal expression data.
Calculate sequence statistics (N50, length distribution, GC content, summary reports) using Biopython. Use when analyzing sequence datasets, generating QC reports, or comparing assemblies.
Modify phylogenetic tree structure using Biopython Bio.Phylo. Use when rooting trees with outgroups or midpoint, pruning taxa, collapsing clades, ladderizing branches, or extracting subtrees.
End-to-end imaging mass cytometry workflow from raw acquisitions to spatial cell analysis. Orchestrates image preprocessing, segmentation, phenotyping, and spatial statistics. Use when analyzing imaging mass cytometry data end-to-end.
Visualize differential expression results using DESeq2/edgeR built-in functions. Covers plotMA, plotDispEsts, plotCounts, plotBCV, sample distance heatmaps, and p-value histograms. Use when visualizing differential expression results.
Handle paired-end FASTQ files (R1/R2) using Biopython. Use when working with Illumina paired reads, synchronizing pairs, interleaving/deinterleaving, or filtering paired data.
Applies a modified Fagan Inspection methodology to systematically resolve persistent bugs and complex issues. Use when multiple previous fix attempts have failed repeatedly, when dealing with intricate system interactions, or when a methodical root c...
通过真实案例创建高质量skill。先找黄金案例和失败案例，归纳什么有效什么无效，再用理论解释为什么。skill是干活的，要从实践中学习，不是从书本中学习。触发词："帮我创建一个skill"、"我想做一个skill来..."
Use when explaining code, technical concepts, or implementation decisions. Provides structured approach to creating clear, understandable explanations tailored to the audience.
Test-driven development (TDD) process used when writing code. Use whenever you are adding any new code, unless the user explicitly asks to skip TDD or the code is exploratory/spike.
Reference patterns for augmented coding with AI. Use when discussing AI coding patterns, anti-patterns, obstacles, context management, steering AI, or looking up Lexler's patterns collection.
Writes tests without mocks using Nullables. Use when writing tests, especially testing code with external I/O (HTTP, files, databases, clocks, random numbers), designing infrastructure wrappers or replacing mocking libraries.
Discover, install, and use MCP tools and agent skills. Use when you need to find MCP servers, securely connect to them, call their tools, or search/install skills from the Smithery registry.
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