227 skills · sorted by relevance
Sort out other people's expectations from actual commitments, reflect on anger, and review living costs against income. This skill helps you examine personal boundaries and the financial room needed to turn down unwanted work.
Patent research and IP landscape: prior-art search, claim mapping, landscape analysis, and freedom-to-operate. Use when conducting a prior-art search, mapping an IP landscape, evaluating patentability, or running an FTO analysis.
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Applies the existentialist and feminist philosophy of Simone de Beauvoir, French philosopher and author of The Second Sex. Reach for this skill whenever the user is grappling with existential dilemmas, moral ambiguity, gender dynamics, societal expectations, or relationship ethics. Trigger this skill for questions about freedom versus responsibility, bodily autonomy, marginalization, or when the user feels trapped by external labels or "immanence." Use this to help the user reclaim their agency, recognize the social construction of their situation, and make authentic choices that expand their transcendence while respecting the interconnected freedom of others.
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Find out whether a chemical series is already claimed, using SureChEMBL's patent-extracted compound corpus and, where a key is available, PatentsView for legal status and assignee history. Use this skill to trace a structure to the patent documents that disclose it, survey an assignee's filings around a target, and understand what the freedom-to-operate question requires that a structure search cannot answer. Also trigger on SureChEMBL, patent chemistry, Markush structure, freedom to operate, composition of matter, assignee, priority date, patent family, or PatentsView.
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Map the intellectual property landscape for a technology domain or product area. Covers patent cluster analysis, white space identification, competitor IP portfolio assessment, freedom-to-operate preliminary screening, and strategic IP positioning recommendations. Use before starting R&D in a new technology area, when evaluating market entry against incumbents with strong patent portfolios, preparing for investment due diligence, informing a patent filing strategy, or assessing freedom-to-operate risk for a new product.
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Generate website design references as separate horizontal images for each section. Keep a consistent palette while varying layouts, spacing, imagery, and calls to action, giving developers or coding agents concrete visual references for implementation.
Explore career choices, business opportunities, and competing goals using frameworks drawn from Naval Ravikant’s public work. Examine how software or content can multiply effort, identify distinctive knowledge, and clarify what wealth and freedom mean for a decision.
Edit videos through conversation, from transcription and take selection to cuts, color adjustments, animated overlays, and subtitles. Confirm an editing plan, review a checked preview, and refine the result before the final render.
Evaluate everyday tasks using a deliberately high personal hourly rate. Review weekly activities, identify tasks to delegate or drop, and examine whether rising spending is keeping you from having more control over your time.
Prepare an initial review of patents that might affect a product launch. Compare product features with individual patent claim elements, record uncertainties and search limits, and produce a memo for patent counsel. It does not determine launch clearance.
Meta-agent that routes bioinformatics requests to specialised sub-skills. Handles file type detection, analysis planning, report generation, and reproducibility export.
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Gene Ontology over-representation analysis using clusterProfiler enrichGO. Use when identifying biological functions enriched in a gene list from differential expression or other analyses. Supports all three ontologies (BP, MF, CC), multiple ID types, and customizable statistical thresholds.
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Preprocess ribosome profiling data including adapter trimming, size selection, rRNA removal, and alignment. Use when preparing Ribo-seq reads for downstream analysis of translation.
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KEGG pathway and module enrichment analysis using clusterProfiler enrichKEGG and enrichMKEGG. Use when identifying metabolic and signaling pathways over-represented in a gene list. Supports 4000+ organisms via KEGG online database.
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Reads, writes, and converts molecular file formats (SMILES, SDF, MOL2, PDB) using RDKit and Open Babel. Handles structure parsing, canonicalization, and full standardization pipeline including sanitization, normalization, and tautomer canonicalization. Use when loading chemical libraries, converting formats, or preparing molecules for analysis.
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Perform geometric calculations on protein structures using Biopython Bio.PDB. Use when measuring distances, angles, and dihedrals, superimposing structures, calculating RMSD, or computing solvent accessible surface area (SASA).
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Build, manage, and search spectral libraries for proteomics. Use when creating or working with spectral libraries for DIA analysis. Covers DDA-based library generation, predicted libraries (Prosit, DeepLC), and library formats.
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Remove sequencing adapters from FASTQ files using Cutadapt and Trimmomatic. Supports single-end and paired-end reads, Illumina TruSeq, Nextera, and custom adapter sequences. Use when FastQC shows adapter contamination or before alignment of short reads.
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Post-translational modification analysis including phosphorylation, acetylation, and ubiquitination. Covers site localization, motif analysis, and quantitative PTM analysis. Use when analyzing phosphoproteomic data or other modification-enriched samples.
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Protein grouping and inference from peptide identifications. Use when resolving protein ambiguity from shared peptides. Handles protein groups and protein-level FDR control using parsimony and probabilistic approaches.
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Taxonomic classification of ASVs using reference databases like SILVA, GTDB, or UNITE. Covers naive Bayes classifiers (DADA2, IDTAXA) and exact matching approaches. Use when assigning taxonomy to ASVs after DADA2 amplicon processing.
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Gene Set Enrichment Analysis using clusterProfiler gseGO and gseKEGG. Use when analyzing ranked gene lists to find coordinated expression changes in gene sets without arbitrary significance cutoffs. Detects subtle but coordinated expression changes.
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Generate and interpret quality reports from FASTQ files using FastQC and MultiQC. Assess per-base quality, adapter content, GC bias, duplication levels, and overrepresented sequences. Use when performing initial QC on raw sequencing data or validating preprocessing results.
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Extract, process, and deduplicate reads using Unique Molecular Identifiers (UMIs) with umi_tools. Use when library prep includes UMIs and accurate molecule counting is needed, such as in single-cell RNA-seq, low-input RNA-seq, or targeted sequencing to distinguish PCR from biological duplicates.
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