Explore skills

Operational runbook and procedure documentation specialist. Use when

Git operations, shell scripting, CI/CD pipelines, and terminal automation. Use for conventional commits, PowerShell/Bash scripting, configuring GitHub Actions, or automating development tooling workflows.

Administers Arch/CachyOS systems, covering pacman, AUR, systemd, boot, desktop, GPU, and gaming. Triggers include 'arch linux', 'cachyos', 'pacman', 'paru', 'mkinitcpio', and 'hyprland', and it is not for Debian, Fedora, or NixOS.

Writes and reviews Ansible playbooks, roles, inventories, Vault, Molecule, and AWX/AAP. Triggered by 'ansible', 'playbook', 'role', 'inventory', 'group_vars', and 'ansible-lint'.

· Write/debug shell commands, scripts, dotfiles, completions for zsh, bash, POSIX sh, fish. Triggers: 'shell', 'script', '.zshrc', '.bashrc', 'alias', 'completion', 'trap'. Not for CI blocks (use ci-cd).

Identify enriched sequence motifs at CLIP-seq binding sites for RBP binding specificity. Use when characterizing the sequence preferences of an RNA-binding protein.

Call protein-RNA binding sites from CLIP-seq BAM with CLIPper, PureCLIP, Skipper, Piranha, omniCLIP, CTK, CLAM, or Paraclu. Use when choosing between coverage-based, HMM-based, beta-binomial window-based, and crosslink-site-based peak callers; applying ENCODE eCLIP thresholds (log2 IP/SMInput >= 3, -log10 p >= 3); deciding when SMInput is mandatory; or reconciling peak-set discordance between call

Comprehensive quality control for CLIP-seq libraries (eCLIP, iCLIP, iCLIP2, PAR-CLIP) covering library complexity (preseq), FRiP, IDR replicate reproducibility, read-distribution metagene, SMInput vs IgG control rationale, rRNA / snoRNA contamination, fragment-length distribution, and ENCODE-compliance thresholds. Use when assessing whether a CLIP library passed, deciding lenient vs stringent peak

Reconstruct ancestral sequences at phylogenetic nodes using PAML and IQ-TREE marginal likelihood methods. Infer ancient protein sequences and trace evolutionary trajectories through sequence history. Use when inferring ancestral states for protein resurrection or tracing evolutionary history.

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,

JACKS (Joint Analysis of CRISPR/Cas9 Knockout Screens) for modeling sgRNA efficacy and gene essentiality. Use when analyzing multiple CRISPR screens simultaneously or when accounting for variable sgRNA efficiency across experiments.

Detects somatic mutations in circulating tumor DNA using variant callers optimized for low allele fractions with UMI-based error suppression. Reliably detects mutations at VAF above 0.5 percent using consensus-based approaches. Use when identifying tumor mutations from plasma DNA or tracking specific variants.