Autonomous research Agent for bioinformatics: 300+ bioinformatics skills, persistent R/Python kernels, autonomous accumulation of user experience, scripts as skills, audit and debate dual gating, self-healing supervision for long tasks, and three-layer long-term memory; autonomously builds knowledge bases, searches and extracts literature, designs research ideas, polishes papers, performs bioinformatics analysis and visualization, and more. Ready to use on Windows/Linux with any OpenAI-compatibl
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Skill Claude Code
A set of rules for deciding when and how an analysis should be challenged by several independent reviewers. It uses different levels of debate depending on uncertainty, failures, conflicts, and the importance of the result.
Skill Claude Code
A deep-research workflow that coordinates literature searches, reviews, systematic reviews, and method or patent prior-art studies. Prior-art research checks what methods or inventions have already been described publicly.
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A workflow for differential-expression analysis in single-cell RNA sequencing. Differential expression compares gene activity between groups to find genes whose measured levels differ.
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Design complementary oligonucleotides with Type IIS restriction enzyme overhangs for Golden Gate assembly based on restriction site analysis of the backbone.
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Design sgRNAs for CRISPR knockout by searching pre-computed sgRNA libraries. Returns optimized guide RNAs for targeting a specific gene.
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Design a single primer within the given sequence window.
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Design Sanger sequencing primers to verify a specific region in a plasmid. First tries to use primers from an existing primer pool. If they cannot fully cover the region, designs additional primers as.
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Detects and annotates somatic mutations in tumor samples compared to matched normal samples using GATK Mutect2 for variant calling, GATK FilterMutectCalls for filtering, and SnpEff for functional anno.
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Detects and characterizes structural variations (SVs) in genomic sequencing data using LUMPY for SV detection followed by annotation with COSMIC and/or ClinVar databases.
Skill Claude CodeCodex
Create branded architecture, IT current-state, flowchart, sequence, state machine, ER/data model, timeline, swimlane, quadrant, radar/spider, loop/flywheel, nested, tree, org chart, layer stack, Venn, pyramid/funnel, bar, line, Gantt and scatter charts, high-level, process, medallion, data flow, DP integration, or DP…
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Simulates restriction enzyme digestion of a DNA sequence and returns the resulting fragments with their properties.
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A biology-analysis workflow for studying how disease changes over time. The available description gives process and review rules but does not specify the data inputs or exact analyses.
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Performs molecular docking using AutoDock Vina to predict binding affinities between small molecules and a receptor protein.
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A document-generation workflow from a biology analysis platform. Its description focuses on required knowledge searches, environment checks, staged script execution, review, and debate before and after analysis.
Skill Claude Code
A single-cell RNA sequencing workflow for detecting and removing doublets, which are droplets containing two cells instead of one. It uses Seurat and DoubletFinder to identify suspicious cells and produce filtered data and diagnostic plots.
Skill Claude Code
A bioinformatics workflow for predicting how diseases or tumors may respond to drugs using gene-expression signatures, drug-sensitivity data, and combination-therapy analysis. IC50 is a measure of how much drug is needed to reduce a measured response by half.
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Estimate radiation absorbed doses to tumor and normal organs for alpha-particle radiotherapeutics using the Medical Internal Radiation Dose (MIRD) schema.
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Estimate cell cycle phase durations using dual-nucleoside pulse labeling data and mathematical modeling.
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Score, embed, and generate DNA sequences with Evo 2, a long-context genomic foundation model. Use this skill when: (1) Computing per-nucleotide or per-sequence likelihoods for variant effect scoring.
Skill Claude Code
A structured workflow for planning and analyzing scientific experiments with statistical and bioinformatics methods. It requires checking references, the computing environment, code, results, and uncertain decisions at each stage.
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Extract text content from a PDF file.
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Extract the text content of a webpage using requests and BeautifulSoup.
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Fetches supplementary information for a paper given its DOI and saves it to a specified directory.
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A file-format conversion tool for moving data between CSV, Excel, TSV, H5AD, MTX, and other common formats. It checks the input structure, performs the conversion, and verifies the resulting file.
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