2.2K skills · sorted by relevance
Use when preparing Australian transaction coding and reconciliations before month-end close or BAS work.
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The shared Codex web-work inbox. Use when a coding agent needs browser work, provider account setup, OAuth or ecommerce portal work, npm publishing, or recovery of an incomplete Vault/account handoff delegated to Codex.
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Configure a Rails project to work with Conductor (parallel coding agents)
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Identifies non-coding RNAs (tRNA, rRNA, snoRNA, snRNA, riboswitches, sRNAs) using Infernal covariance-model search against Rfam, tRNAscan-SE 2.0 for tRNA, barrnap for rRNA, and ARAGORN for tmRNA, plus the small-RNA-seq boundary for miRNA and the transcript-assembly boundary for lncRNA. Covers the structure-conserved-not-sequence-conserved principle (why BLAST fails), GA-threshold and clan-competition correctness, tRNAscan-SE domain modes and pseudogene flags, rDNA copy-number collapse, and why homology annotation is a recall floor. Use when performing genome-wide ncRNA annotation, choosing the right tool for an RNA class, or interpreting ncRNA counts.
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Predicts protein-coding gene structures (exons, introns, UTRs) in eukaryotic genomes with BRAKER3 (RNA-seq + protein evidence), BRAKER1/BRAKER2, GALBA (protein-only), Funannotate (fungi), GeMoMa (homology projection), or Helixer/Tiberius (deep-learning ab initio). Covers the evidence-first tool decision, mandatory soft-masking, the training-set-quality-dominates principle, OrthoDB clade-partition selection, the one-isoform-per-locus and missing-UTR traps, merge/split errors, and reference bias against orphan genes. Use when annotating a newly assembled eukaryotic genome, choosing a gene-prediction pipeline based on available evidence, or diagnosing a poor annotation.
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Aligns sample metadata with count matrices and constructs design matrices for downstream DE, handling the alphabetical-reference-level trap (relevel BEFORE DESeq), LRT reduced-model rules, the interaction-term resultsNames trap, continuous-covariate scaling and splines, repeated measures via duplicateCorrelation or dream, high-cardinality categorical pseudo-singular designs, sample swap detection via XIST/RPS4Y1 expression and somalier/NGSCheckMate genotypes, SABV (sex-as-biological-variable) mandate, Simpson's-paradox collapsing of technical replicates, and the `~ 0 + group` parameterization for clean contrasts. Use when building a design matrix, troubleshooting reversed fold-change direction, encoding paired or repeated-measures designs, detecting sample swaps, deciding sex-as-covariate, or aggregating technical replicates.
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Assesses the quality and completeness of a genome annotation with BUSCO (conserved single-copy ortholog recovery), OMArk (proteome completeness, consistency, and contamination), CheckM2 (prokaryotic completeness/contamination), and a gene-set sanity panel (gene count, mono-exonic fraction, protein-length distribution, mRNA:gene ratio, coding density). Covers the assembly-BUSCO-vs-proteome-BUSCO diagnostic, what BUSCO-Duplicated really means, why gene count is a vanity metric, and the QC of transferred annotations. Use when judging whether an annotation is good enough to publish or submit, diagnosing a suspect annotation, or comparing annotation completeness across pipelines.
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Select colormaps and qualitative palettes for scientific figures using perceptual-uniformity, color-vision-deficiency safety, and luminance-monotonicity criteria. Covers Crameri scientific colormaps, viridis/cividis/magma, Okabe-Ito categorical, ColorBrewer, and the rainbow/jet critique. Use when choosing palettes for heatmaps, scatter, networks, or any encoding where color carries quantitative or categorical meaning.
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Build sequence logos from aligned DNA, RNA, or protein motifs using ggseqlogo (R), Logomaker (Python), or WebLogo with explicit bits vs probability encoding, background-frequency correction, custom alphabets, and multi-logo stacking. Use when visualizing motif PWMs (TF binding, splice sites, CRISPR spacers), aligned-position composition, or comparing two motif sets.
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Plot per-group distributions of continuous data using boxplots, violins, beeswarms, quasirandom jitter, and raincloud plots with sample-size honesty (Weissgerber 2015), KDE-bandwidth awareness, and N-aware encoding choices. Use when comparing distributions across a small number of groups — expression per cluster, biomarker per arm, scores per condition — and the bar-of-mean default is misleading.
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Detect positive (diversifying / episodic / pervasive) selection using codon dN/dS frameworks. Implements PAML codeml site models (M0/M1a/M2a/M7/M8/M8a), branch models, branch-site model A (Zhang 2005), and HyPhy methods (BUSTED, BUSTED-S, BUSTED-MH, BUSTED-PH, MEME, FEL, FUBAR, aBSREL, SLAC, RELAX, GARD, FUBAR-MH). Includes McDonald-Kreitman framework (asymptotic alpha, impMKT, polyDFE, DFE-alpha, GRAPES) for within-species + divergence inference, RERconverge for trait-correlated rate shifts, CSUBST for convergent substitution, and PhyloAcc for accelerated noncoding evolution. Use when testing adaptive evolution at codons, branches, or full gene; running GARD recombination pre-screen; controlling alignment-error and gBGC false positives; reconciling PAML vs HyPhy results; or performing genome-scale selection scans.
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Analyzes differential transcript usage (DTU) and isoform switches with functional consequence prediction (NMD via 50nt rule, ORF disruption, protein domain loss/gain, signal peptide changes, IDR alterations, coding-potential shifts). Tools include IsoformSwitchAnalyzeR v2 (auto-selects satuRn for >5 reps else DEXSeq), the manual DRIMSeq -> DEXSeq/satuRn -> stageR DTU pipeline, and fishpond/swish for inferential-uncertainty-aware DTE. Distinguishes DTU from DGE and DTE; integrates external annotators (CPC2, Pfam, SignalP, IUPred2A or DeepTMHMM). Use when investigating how splicing differences alter protein function or trigger NMD-mediated degradation.
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Provider account and authenticator setup through Matrx Vault. Use when creating a service account, saving its login, enrolling 2FA, or verifying agent sign-in with Vault credentials.
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Use when implementing authentication, authorization, JWT tokens, security filters, password encoding, or any Spring Security configuration. Covers stateless JWT auth, token rotation, RBAC, and method-level security.
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Picks the model a coding agent uses when a test or browser check sends an AI call. Use when choosing a model for any test, UI check, bench, or agent run, or when a test names Opus, Sonnet, Fable, Astra, or any model by habit.
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Use this skill whenever the user wants to create, read, edit, or manipulate Word documents (.docx) or Word templates (.dotx). Triggers include: any mention of Microsoft Word Documents, such as 'Word doc', 'word document', '.docx', '.dotx', 'microsoft doc'. Also use when extracting or reorganizing content from .docx or .dotx files, inserting or replacing images in documents, find-and-replace in Word files, working with tracked changes or comments, or converting content into a polished Word document. If the user asks for a deliverable as a Word or .docx file (to download, email or print), use this skill. However, if they ask for a document, page, report, memo, or notes WITHOUT naming a file format and the session offers Claude's own dedicated document or page skill or connector, use that instead, even if they will email or print it. Do NOT use for PDFs, spreadsheets, Google Docs, or coding unrelated to document generation.
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Conduct a retrospective on a coding session.
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Expert in secure backend coding practices specializing in input validation, authentication, and API security. Use PROACTIVELY for backend security implementations or security code reviews.
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Turn a one-line objective into a step-by-step construction plan any coding agent can execute cold. Each step has a self-contained context brief — a fresh agent in a new session can pick up any step without reading prior steps.
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Azure Maps SDK for .NET. Location-based services including geocoding, routing, rendering, geolocation, and weather. Use for address search, directions, map tiles, IP geolocation, and weather data.
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Ask which skill or flow fits your situation. A router over the user-invoked skills in this repo.
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AI-powered E2E web testing — eyes and hands for AI coding tools. Declarative YAML scenarios, Playwright execution, visual matching (OpenCV + OCR), platform auto-detection (Flutter/React/Vue), learning DB. Install: npx skills add ksgisang/awt-skill --skill awt -g
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Design patterns for building autonomous coding agents, inspired by [Cline](https://github.com/cline/cline) and [OpenAI Codex](https://github.com/openai/codex).
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Route agent work through AccInt's MCP memory loop: retrieve prior outcomes, resolve frames, and close commitments with evidence.
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