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Writes the full Results section of a biomedical manuscript from a sufficiently clear result structure, figure inventory, or analysis summary while preserving evidence boundaries and result hierarchy.
Statistical differential expression analysis using DESeq2 or edgeR in R, with support for count matrix or tximport input.
Generate gene-level read count matrices from aligned BAMs using featureCounts or HTSeq-count.
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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 …
Normalization, highly variable gene selection, PCA, UMAP, and Leiden/Louvain clustering of single-cell RNA-seq data.
Ambient RNA removal, doublet detection, and cell filtering for single-cell RNA-seq count matrices.
Search CNCB Genome Sequence Archive (GSA) for sequencing runs, experiments, studies, and samples deposited at the China National Center for Bioinformation.
Builds prioritized manuscript revision plans for major or minor revisions by separating comments that require experiments, analyses, clarification, restructuring, or wording changes.
Gene set enrichment and over-representation analysis using clusterProfiler, gseapy, or fgsea, with GO, KEGG, and Reactome pathway databases.
Alignment-free transcript-level quantification using Salmon or kallisto for fast and accurate RNA-seq expression estimates.
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…
Marker-based and reference-based cell type annotation of single-cell RNA-seq clusters using SingleR, Azimuth, or manual curation.
Single-cell differential expression analysis using Wilcoxon rank-sum tests and pseudobulk approaches with DESeq2 or edgeR.
Search the EMBL-EBI European Nucleotide Archive (ENA) for sequencing studies, runs, samples, and experiments using the ENA Portal REST API.
Search NCBI Datasets for genome assemblies, genes, taxonomy records, and virus genomes using the NCBI Datasets CLI or REST API.
RNA-seq-specific alignment quality assessment using RSeQC and Qualimap for gene body coverage, strandedness, and rRNA contamination.
Splice-aware alignment of RNA-seq reads to a reference genome using STAR or HISAT2.
Use natural language to prepare, run, and interpret standalone rpsblast, rpstblastn, and rpsbproc workflows against NCBI CDD assets.
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…
Generate feature-barcode count matrices from raw scRNA-seq FASTQ files using Cell Ranger, STARsolo, or alevin-fry.
Multi-sample batch correction and integration of single-cell RNA-seq datasets using Harmony, Seurat CCA/RPCA, or scVI.
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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