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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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personTashanworldAPI key: unconfirmed
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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slurm-job-script-generator
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table-narrative-writer
Converts biomedical table content into clear manuscript or presentation narrative by prioritizing meaningful patterns, contrasts, and interpretation boundaries rather than restating every number.
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personTashanworldAPI key: unconfirmed
word-flowchart
Create Word-style flowcharts in Graphviz DOT with black/white styling, orthogonal arrows, and clean alignment. Use when converting text or images into flowcharts, refining DOT layout/spacing, enforcin…
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personTashanworldAPI key: unconfirmed
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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personTashanworldAPI key: unconfirmed
social-science-reviewer
Diagnose, review, and strengthen social-science manuscripts, research designs, literature reviews, grant proposals, thesis chapters, methods sections, revision plans, and submission-readiness decision…
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time-stepping
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workflow-engine-mapper
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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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personTashanworldAPI key: unconfirmed
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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solublempnn
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title-and-abstract-optimizer
Optimizes manuscript titles and abstracts for information density, factual accuracy, and submission fit in biomedical research writing.
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personTashanworldAPI key: unconfirmed
writing-commenter
Review research writing by leaving inline comments on logic, notation, narrative flow, positioning, and editorial impact. Use when Codex needs to annotate a paper or draft with reader-facing comments …
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