Coding & Dev Tools

gptomics Bundle

Quantifies known miRNAs, isomiRs, tRFs, and A-to-I editing fast with miRge3.0 by aligning collapsed reads to curated miRBase or MirGeneDB libraries. Use when choosing miRBase versus MirGeneDB as the reference; deciding whether to collapse isomiRs to the parent miRNA or keep 5'-isomiRs separate (they shift the seed and retarget); confirming the organism is among the six supported species; or remembering that RPM output is for display only and raw counts go to DESeq2/edgeR.

gptomics Bundle

Generate alignment statistics using samtools flagstat, stats, depth, coverage, and mosdepth. Use when assessing alignment quality, calculating coverage, or generating QC reports.

gptomics Bundle

View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. Use when inspecting alignments, converting between formats, or understanding alignment file structure.

gptomics Bundle

Align protein structures using Foldseek 3Di, TM-align, US-align, DALI, or Foldmason for structural MSA. Predict, score, and superpose backbone coordinates when sequence identity is below the twilight zone or remote-homology detection is required. Use when sequence MSA fails (<25% identity), when the dark proteome is the target, when AlphaFoldDB / ESM Atlas search is needed, or when structural superposition is the goal.

gptomics Bundle

Builds QSAR / QSPR models using chemprop D-MPNN, MolFormer, Uni-Mol, ChemBERTa, random forest baselines, and Gaussian processes with explicit handling of OECD 5 principles, applicability domain (kNN, leverage, conformal prediction, Mahalanobis), scaffold-balanced splits, ensemble uncertainty, calibration (Platt, isotonic), feature importance (SHAP, atomic attribution), and prospective validation. Use when building target-specific predictive models from in-house bioassay data, ADMET endpoints, or selectivity profiles.

gptomics Bundle

Visualizes ChIP-seq data using deepTools (computeMatrix, plotHeatmap, plotProfile, bamCoverage, bamCompare), pyGenomeTracks (modern INI-driven track plots), Gviz (R browser-style), EnrichedHeatmap (ComplexHeatmap-based), ChIPseeker tag heatmaps, and IGV batch screenshots. Handles bigWig normalization choices (CPM, BPM, RPGC, spike-in scaled), bamCompare operations (log2 ratio, subtract) with SES scaling, k-means clustering of heatmaps for biological subgrouping, and spike-in-scaled tracks for global-shift experiments. Use when generating publication-quality ChIP-seq signal heatmaps, profile plots, genome-browser tracks, or comparing samples visually.

sboghossian-mini-claude-for-legal Skill

Use when a site visitor's search query or navigation intent matches a named AI feature, skill, calculator, or tool library within the legal AI platform. Routes the user to the dedicated feature page for that capability rather than returning a generic search result. Applies to all jurisdictions and user types interacting with the platform's public-facing site.

sboghossian-mini-claude-for-legal Skill

Use when defining ideal customer profiles, informing product prioritisation, tailoring messaging, or training sales teams on Louis's target buyer segments. Covers four primary MENA ICP tiers — MENA law firms (5–50 lawyers), MENA in-house counsel, MENA solo practitioners, and MENA law students — plus the secondary Western-firms segment. Internal use only.

sboghossian-mini-claude-for-legal Skill

Use when an investor, sophisticated buyer, strategic partner, or senior decision-maker asks for a substantive overview of HAQQ's market thesis, product vision, and competitive defensibility. Provides the narrative, supporting data points, and framing for the general whitepaper targeted at high-context audiences evaluating HAQQ as a company and platform.

sboghossian-mini-claude-for-legal Skill

Use when asked to draft a cease-and-desist (C&D) letter demanding that a recipient stop specified infringing, wrongful, or harmful conduct. Covers the most common C&D use cases — trademark/IP infringement, defamation, breach of contract, harassment, and unfair competition — with a complete document structure, tone guidance, jurisdictional enforceability notes for MENA and common-law systems, and the DMCA cross-reference for online infringement.

sboghossian-mini-claude-for-legal Skill

Use when asked to draft a commercial lease for office, retail, or industrial premises. Covers the full clause set — premises, use, rent and service charge, VAT, rent review, fit-out and makegood, repair, insurance, alienation, forfeiture, and quiet enjoyment — with jurisdiction-specific notes for UAE onshore, DIFC/ADGM (FRI lease norms), KSA (15% VAT), Lebanon (commercial lease law and fonds de commerce protections), and Egypt. Required inputs include landlord, tenant, premises, rent, term, use, and jurisdiction.

sboghossian-mini-claude-for-legal Skill

Use when asked to draft a convertible promissory note — a debt instrument that converts into equity on a qualified financing event. Covers required inputs (principal, interest, maturity, valuation cap, discount), the conversion mechanics, change-of-control treatment, events of default, the note-vs-SAFE structural choice, and MENA-specific considerations including interest structuring under Sharia-compliant frameworks and jurisdiction availability of SAFEs.

sboghossian-mini-claude-for-legal Skill

Use when generating WHEREAS recital clauses (or civil-law préambule / تمهيد) for any contract. Provides the pattern for 3-7 recitals that establish parties' identities, transaction purpose, and mutual intent, followed by the formal consideration language. Adapts between common-law WHEREAS-clause format and civil-law narrative preamble traditions used in LB, FR, UAE onshore, KSA, and EG. Triggers on "recitals", "whereas clauses", "preamble", "background", or "write the opening of the contract" requests.

sboghossian-mini-claude-for-legal Skill

Use when drafting Terms of Service, Terms of Use, or Terms and Conditions for a website, app, SaaS platform, or marketplace. Covers all standard sections including acceptance, eligibility, user content licensing, IP ownership, disclaimers, limitation of liability, indemnification, termination, and modification. Addresses jurisdiction-specific consumer protection overlays including EU Directive 2011/83, CCPA arbitration mechanics, and UAE Federal Law 4/2022 and KSA Consumer Protection Law for MENA operators. Always pair with a Privacy Policy.

sboghossian-mini-claude-for-legal Skill

Use when a lawyer or legal team needs to surface, organize, and monitor all deadlines on an active matter — including statutory limitation periods, court-ordered deadlines, internal milestones, and client-driven dates. For each deadline the skill assigns an owner, defines pre-deadline tasks, documents consequences of a miss, and triggers a graduated escalation chain (T-14/7/3/1). Pairs with the date-tool deadline calculator for jurisdiction-aware holiday exclusion.

oimiragieo Bundle

Configurable regex-based alert system for detecting patterns in tool calls and session activity. Supports error triggers, content regex matching, token threshold triggers, and pattern detection with configurable actions.

oimiragieo Bundle

Python backend expert including Django, FastAPI, Flask, SQLAlchemy, and async patterns

oimiragieo Bundle

Process and act on code review feedback. Use when receiving review results.

gptomics Bundle

Reads, queries, and writes bigWig indexed binary signal tracks (coverage, fold-change, conservation, methylation-rate) with pyBigWig (Python) and the UCSC Kent tools (bedGraphToBigWig, bigWigToBedGraph, bigWigInfo, bigWigSummary, bigWigAverageOverBed) and deepTools (multiBigwigSummary, computeMatrix, bigwigCompare). Covers the central trap that a wide query returns a precomputed zoom-level summary (by default the mean, which annihilates narrow peaks) not per-base data, when exact=True/values() is mandatory, the NaN-not-zero gap-handling fork, choosing mean vs max vs sum vs coverage by biological question, and the sorted-bedGraph plus chrom.sizes build requirement. Use when extracting signal at regions, computing mean signal per gene/peak, building a browser track from bedGraph, comparing tracks, or building TSS/gene-body metaprofiles.

gptomics Bundle

Compares Hi-C contact maps between conditions across the right scale -- differential bin-pair contacts (multiHiCcompare, diffHic), differential A/B compartments (dcHiC), differential TAD boundaries (delta insulation), and differential loops (diffloop, DiffHiChIP) -- with distance-stratified between-sample normalization, replicate-aware NB-GLM FDR, HiCRep SCC reproducibility gating, and CNV correction for cancer/aneuploid samples. Use when comparing Hi-C between treatment and control, finding differential contacts/compartments/boundaries/loops, normalizing two maps of unequal depth, choosing a replicate-aware test, gating replicates with SCC, or correcting copy-number artifacts before a tumor-vs-normal comparison.

gptomics Bundle

Assigns taxonomy to amplicon ASVs/OTUs (16S, ITS, 18S) with a classifier conditioned on a reference database and primer region - DADA2 assignTaxonomy + addSpecies (RDP naive Bayes), DECIPHER IDTAXA, and QIIME2 q2-feature-classifier (classify-sklearn naive Bayes, classify-consensus-vsearch alignment-consensus). Covers region-specific training (extract-reads, fit-classifier-naive-bayes), why a full-length classifier fabricates calls on a V4 read, the scikit-learn version-pinning trap on pre-trained .qza classifiers, confidence thresholds (classify-sklearn 0.7, assignTaxonomy minBoot 50), and choosing SILVA/GTDB/Greengenes2/UNITE/PR2/RDP. Use when classifying ASVs after DADA2, picking a reference database, training a region-matched classifier, setting a confidence threshold, or deciding whether a 16S species call is defensible (usually not - genus at best). For shotgun read classification see metagenomics/kraken-classification and metagenomics/metaphlan-profiling.

gptomics Bundle

Runs Gene Ontology over-representation analysis (ORA) on a gene LIST with clusterProfiler enrichGO, the one-sided hypergeometric/Fisher 2x2 test phyper(k-1, M, N-M, n, lower.tail=FALSE). Covers why the BACKGROUND universe (not the gene list) is the null and decides significance, why omitting universe= is a bug, why enrichGO defaults to ont='MF' not 'BP', why pvalueCutoff filters p.adjust not raw p, why ORA discards effect magnitude and inherits GO-DAG true-path redundancy (simplify, topGO), why RNA-seq gene-length bias inflates long-gene terms (GOseq Wallenius), plus GeneRatio/BgRatio, bitr ID mapping, minGSSize/maxGSSize, groupGO. Use when a pre-selected gene list (DE hits, co-expression module, screen, GWAS-mapped) needs GO annotation. For a ranked no-cutoff analysis see gsea; for other databases see kegg-pathways, reactome-pathways, wikipathways; DE source is differential-expression/de-results; plots in enrichment-visualization.

gptomics Bundle

Preprocess ribosome profiling reads with UMI handling, adapter trimming, contaminant/rRNA depletion, and footprint-aware alignment. Use when preparing Ribo-seq FASTQ for periodicity QC, ORF detection, translation efficiency, or stalling analysis, or when deciding how to deduplicate, which aligner to use, or how to size-select ribosome-protected fragments.

gptomics Bundle

Detect cluster marker genes and assign manual cell type labels in single-cell RNA-seq using Scanpy (Python) and Seurat (R). Use when finding genes that distinguish clusters, ranking markers for annotation, scoring gene signatures, hand-labeling clusters, or deciding between Wilcoxon marker ranking and pseudobulk condition DE.

oimiragieo Skill

Fixes skill tests, catalog mismatches, missing workflows, and improves ecosystem gate scores

oimiragieo Bundle

Use ast-grep for AST-based code pattern matching.

oimiragieo Bundle

Rules for creating and maintaining Dockerfiles.

sboghossian-mini-claude-for-legal Skill

Use when defining, measuring, or debugging latency Service Level Objectives (SLOs) for individual legal AI skills. Different skills have different acceptable latency — a conflict check must be fast; a full engagement letter draft can take longer. Covers the SLO definition framework, measurement approach, p50/p95/p99 targets by skill tier, alerting setup, and common latency root causes in legal AI products.

sboghossian-mini-claude-for-legal Skill

Use when the public-facing assistant (Justice on haqq.ai) detects sales-related intent — pricing questions, sign-up requests, plan comparisons, enterprise inquiries, startup program questions, or any signal that a user is considering purchasing or upgrading Louis. Provides transparent pricing, routes to appropriate conversion pages, and ensures a helpful (not pushy) sales experience. Covers all jurisdictions.

sboghossian-mini-claude-for-legal Skill

Use when advising on Lebanese banking regulation, including Banque du Liban (BDL) oversight, banking license types, the ongoing financial crisis and its legal consequences (capital controls, multi-tier exchange rates, bank restructuring), AML obligations under the Special Investigation Commission, bank secrecy reforms, and IMF-linked reform expectations. Essential context for any cross-border transaction involving Lebanese banks or Lebanese-domiciled entities.

sboghossian-mini-claude-for-legal Skill

Use when advising on Saudi criminal procedure, including arrest and detention rights, the role of the Public Prosecution (Niyaba 'Amma), investigation procedures, right to counsel, bail and pre-trial detention, the court structure (criminal courts, Court of Appeal, Supreme Court), trial procedure, sentencing under Sharia categories (hudud, qisas, ta'zir), and the special procedures for financial crimes and cybercrime. Essential for any client facing criminal exposure in Saudi Arabia.

sboghossian-mini-claude-for-legal Skill

Use when advising on UAE criminal procedure under the Federal Penal Code and Code of Criminal Procedure, including arrest and detention rights, the role of the Public Prosecution, bail, court structure (Criminal Courts of First Instance, Court of Appeal, Court of Cassation, Federal Supreme Court), DIFC/ADGM civil-only jurisdiction, cybercrime, financial crime, AML criminal exposure, drug offences, and the distinct rules applicable in free zone vs onshore contexts. Essential for any individual or corporate facing criminal exposure in the UAE.

sboghossian-mini-claude-for-legal Skill

Use when a matter involves financial services licensing, fintech regulation, or establishing a regulated entity in the Abu Dhabi Global Market (ADGM). Covers the Financial Services and Markets Regulations 2015 (FSMR) administered by the Financial Services Regulatory Authority (FSRA), ADGM fintech-specific pathways (RegLab sandbox, Digital Assets Framework), license categories (payment services, investment management, lending, crowdfunding, crypto assets), capital requirements, and comparison with DIFC licensing. Triggers on ADGM fintech license, FSRA application, ADGM RegLab, ADGM crypto, or ADGM financial services questions.

sboghossian-mini-claude-for-legal Skill

Use when a matter involves financial services licensing, fintech regulation, payment services, investment management, or establishing a regulated financial entity in the Dubai International Financial Centre (DIFC). Covers DFSA-regulated activities, the Innovation Testing License (ITL) sandbox, capital requirements, crypto-asset services (DFSA crypto regime), AML/CFT obligations, comparison with ADGM, and the typical 4–9 month setup process. Triggers on DIFC fintech license, DFSA application, DIFC ITL sandbox, DIFC crypto, or DIFC financial services questions.

sboghossian-mini-claude-for-legal Skill

Use when a matter involves insurance regulation, takaful (Islamic insurance) structures, mandatory insurance requirements, or insurance contract drafting in MENA jurisdictions (Saudi Arabia, UAE, Lebanon, Egypt, DIFC/ADGM). Covers the distinction between conventional insurance and takaful models (wakala and mudaraba), regulatory bodies (SAMA/CHI for KSA, CBUAE/SCA for UAE, SFC/MOF for LB, FRA for Egypt), mandatory insurance classes, and key insurance contract drafting points. Triggers on takaful structure, insurance license MENA, mandatory insurance KSA/UAE, insurance dispute MENA, or reinsurance MENA questions.

sboghossian-mini-claude-for-legal Skill

Use when a matter involves Sharia-compliant financial products, Islamic banking structures, sukuk issuance, takaful, or the use of AAOIFI standards. Covers the major Islamic finance structures (murabaha, ijara, mudaraba, musharaka, sukuk, tawarruq, wakala, salam, istisna), compliance markers for drafting, AAOIFI and IFSB standard-setting roles, Sharia Supervisory Board requirements, and the DIFC/ADGM Islamic finance overlay. Relevant for any transaction involving KSA or UAE onshore parties, Islamic banks, halal investment funds, or Sharia certification. Triggers on Islamic finance, sukuk, murabaha, AAOIFI, Sharia-compliant, takaful, halal investment, or Islamic banking questions.