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rnaseq-functional-enrichment
Gene set enrichment and over-representation analysis using clusterProfiler, gseapy, or fgsea, with GO, KEGG, and Reactome pathway databases.
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Skill Directory
AI Skill Directory
Browse curated skills with source links, package snapshots, README assets and install signals in one calm, searchable catalog.
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rnaseq-transcript-quantification
Alignment-free transcript-level quantification using Salmon or kallisto for fast and accurate RNA-seq expression estimates.
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sci-review
Specialized workflows for drafting, refining, and responding to academic literature reviews and peer review feedback. Use this skill for literature review outlines, research-gap synthesis, reviewer re…
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scrnaseq-cell-type-annotation
Marker-based and reference-based cell type annotation of single-cell RNA-seq clusters using SingleR, Azimuth, or manual curation.
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scrnaseq-differential-expression
Single-cell differential expression analysis using Wilcoxon rank-sum tests and pseudobulk approaches with DESeq2 or edgeR.
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search-ena
Search the EMBL-EBI European Nucleotide Archive (ENA) for sequencing studies, runs, samples, and experiments using the ENA Portal REST API.
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search-ncbi-datasets
Search NCBI Datasets for genome assemblies, genes, taxonomy records, and virus genomes using the NCBI Datasets CLI or REST API.
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simulation-validator
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rnaseq-read-alignment
Splice-aware alignment of RNA-seq reads to a reference genome using STAR or HISAT2.
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rpsblast-assistant
Use natural language to prepare, run, and interpret standalone rpsblast, rpstblastn, and rpsbproc workflows against NCBI CDD assets.
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scientific-documentation
Writing senior-level documentation for scientific software. Covers NumPy/Google docstring styles, type hints as documentation, README structure for research tools, Sphinx vs MkDocs setup, API referenc…
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scrnaseq-cellranger-count
Generate feature-barcode count matrices from raw scRNA-seq FASTQ files using Cell Ranger, STARsolo, or alevin-fry.
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scrnaseq-integration
Multi-sample batch correction and integration of single-cell RNA-seq datasets using Harmony, Seurat CCA/RPCA, or scVI.
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search-geo
Search NCBI Gene Expression Omnibus (GEO) for expression datasets, series, samples, and platforms using E-utilities or the GEO query API.
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simulation-failure-triage
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single-cell-rna-qc
Performs quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations. Use when users request QC analysis, fi…
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rnaseq-read-counting
Generate gene-level read count matrices from aligned BAMs using featureCounts or HTSeq-count.
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scgpt
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scientific-problem-selection
This skill should be used when scientists need help with research problem selection, project ideation, troubleshooting stuck projects, or strategic scientific decisions. Use this skill when users ask …
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scrnaseq-clustering
Normalization, highly variable gene selection, PCA, UMAP, and Leiden/Louvain clustering of single-cell RNA-seq data.
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scrnaseq-quality-control
Ambient RNA removal, doublet detection, and cell filtering for single-cell RNA-seq count matrices.
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search-gsa
Search CNCB Genome Sequence Archive (GSA) for sequencing runs, experiments, studies, and samples deposited at the China National Center for Bioinformation.
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simulation-orchestrator
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slide-deck-for-lab-meeting
Structures research progress into focused and actionable slides for lab meetings or project reviews without inventing missing content.
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