Data & Analytics

gptomics Bundle

Handles BED-format genomic intervals (BED3 through BED12, narrowPeak/broadPeak) and the coordinate-system substrate the whole interval category rests on, with bedtools (CLI) and pybedtools/pyranges/pandas (Python). Covers the 0-based half-open vs 1-based-closed convention boundary and the start-1/end-unchanged conversion, the silent failures (chrom-name mismatch, CRLF, lexicographic-vs-version sort under -sorted), genome/chrom.sizes generation, sorting contracts, BED12 block invariants, validation, makewindows, cross-assembly liftover (liftOver/CrossMap), and BED<->VCF/BAM/FASTA conversion. Use when reading, creating, validating, sorting, lifting between genome builds, or converting interval files, preparing inputs for bedtools/tabix/bigBed, or debugging an off-by-one or empty-overlap result.

intent-solutions-io Bundle

Analyzes data sources and generates Nixtla-compatible schema transformations. Infers column mappings, creates transformation modules for CSV/SQL/Parquet/dbt sources, generates schema contracts, and validates data quality. Activates when user needs data transformation, schema mapping, column inference, or Nixtla format conversion.

intent-solutions-io Bundle

This skill enables Claude to perform automated fuzz testing on APIs to discover vulnerabilities, crashes, and unexpected behavior. It leverages malformed inputs, boundary values, and random payloads to generate comprehensive fuzz test suites. Use this skill when you need to identify potential SQL injection, XSS, command injection vulnerabilities, input validation failures, and edge cases in APIs. Trigger this skill by requesting fuzz testing, vulnerability scanning, or security analysis of an API. The skill is invoked using the `/fuzz-api` command.

gptomics Bundle

Combine, split, sort, intersect, and subset VCF/BCF files with bcftools merge, concat, isec, sort, view, and reheader. Use when merging different samples into a cohort VCF, concatenating per-chromosome or per-region call sets for the same samples, intersecting or complementing call sets from different callers, subsetting samples/regions, harmonizing sample names and

intent-solutions-io Skill

This skill analyzes and optimizes SQL queries for improved performance. It identifies potential bottlenecks, suggests optimal indexes, and proposes query rewrites. Use this when the user mentions "optimize SQL query", "improve SQL performance", "SQL query optimization", "slow SQL query", or asks for help with "SQL indexing". The skill helps enhance database efficiency by analyzing query structure, recommending indexes, and reviewing execution plans.

gptomics Bundle

Maps between gene identifier systems (Ensembl, Entrez, HGNC symbol, UniProt, RefSeq, MANE) using AnnotationDbi, biomaRt, mygene, pyensembl, and Ensembl REST. Encodes Ensembl version stripping with GENCODE _PAR_Y preservation, the Ziemann 2016 Excel autocorrect debacle and Bruford 2020 HGNC renames (SEPT*->SEPTIN*, MARCH*->MARCHF*, MARC*->MTARC*, DEC1->DELEC1), OCT4/POU5F1 alias resolution, biomaRt archive endpoints for release pinning, the `filters` (plural) gotcha, MANE Select for clinical reporting, cross-species orthology via Ensembl Compara / OMA / OrthoDB, and tx2gene construction for tximport. Use when converting gene IDs across systems, handling renamed symbols, building tx2gene, pinning to a specific Ensembl release for reproducibility, or mapping cross-species orthologs.

sboghossian-mini-claude-for-legal Skill

Use when analysing conversion drop-off in a defined product funnel (signup → first chat → first draft → first save → upgrade) using PostHog. Produces step-by-step conversion percentages, median time-to-step, cohort-segmented drop-off reasons, path analysis between steps, and three ranked hypotheses for the biggest leak — each paired with an actionable experiment recommendation.

intent-solutions-io Skill

This skill automates security vulnerability testing. It is triggered when the user requests security assessments, penetration tests, or vulnerability scans. The skill covers OWASP Top 10 vulnerabilities, SQL injection, XSS, CSRF, authentication issues, and authorization flaws. Use this skill when the user mentions "security test", "vulnerability scan", "OWASP", "SQL injection", "XSS", "CSRF", "authentication", or "authorization" in the context of application or API testing.

intent-solutions-io Skill

This skill enables Claude to automatically scan source code for potential input validation vulnerabilities. It identifies areas where user-supplied data is not properly sanitized or validated before being used in operations, which could lead to security exploits like SQL injection, cross-site scripting (XSS), or command injection. Use this skill when the user asks to "scan for input validation issues", "check input sanitization", "find potential XSS vulnerabilities", or similar requests related to securing user input. It is particularly useful during code reviews, security audits, and when hardening applications against common web vulnerabilities. The skill leverages the input-validation-scanner plugin to perform the analysis.

intent-solutions-io Skill

This skill enables Claude to perform comprehensive database security scans using the database-security-scanner plugin. It is triggered when the user requests a security assessment of a database, including identifying vulnerabilities like weak passwords, SQL injection risks, and insecure configurations. The skill leverages OWASP guidelines to ensure thorough coverage and provides remediation suggestions. Use this skill when the user asks to "scan database security", "check database for vulnerabilities", "perform OWASP compliance check on database", or "assess database security posture". The plugin supports PostgreSQL and MySQL.

gptomics Bundle

Assign cell types from marker expression in IMC/MIBI data using clustering (PhenoGraph/FlowSOM/Leiden/Pixie), marker-based probabilistic classifiers (Astir), or image-context CNNs (CellSighter), covering the double-positive segmentation artifact, lineage-vs-state markers, the two spillover types, and why a "cell type" in imaging is conditioned on a segmentation guess. Use when phenotyping segmented IMC cells, choosing clustering vs classification, diagnosing implausible double-positive populations, separating lineage from functional markers, or transferring labels across a cohort.

autohandai-community-skills Bundle

This skill covers detecting cyber attacks targeting Supervisory Control and Data Acquisition (SCADA) systems including man-in-the-middle attacks on industrial protocols, unauthorized command injection into PLCs, HMI compromise, historian data manipulation, and denial-of-service against control system communications. It leverages OT-specific intrusion detection systems, industrial protocol anomaly detection, and process data analytics to identify attacks that traditional IT security tools miss.

gptomics Bundle

Estimates haplotype phase from population linkage disequilibrium with SHAPEIT5, SHAPEIT4, Eagle2, or Beagle - turning unphased genotypes (0/1) into phased haplotypes (0|1) for imputation input, compound-heterozygote calls, HLA typing, or population genetics. Covers why statistical phase is an INFERENCE (not a measurement) whose error concentrates at rare variants, why a genome-wide switch-error rate hides catastrophic rare-variant error and must be reported MAC-stratified, the SHAPEIT5 common-scaffold-then-rare design (phase_common, ligate, phase_rare, switch), reference-based vs within-cohort phasing, the build-matched genetic map, chrX male-haploid handling, and the switch-vs-flip-vs-Hamming distinction. Use when phasing genotypes before imputation, for compound-het/ASE/HLA, or benchmarking against trios. Read-backed / molecular phasing (long reads, Hi-C) is long-read-sequencing/haplotype-phasing; panel choice is reference-panels; imputation is genotype-imputation.

autohandai-community-skills Bundle

Implement User and Entity Behavior Analytics using Elasticsearch/OpenSearch to build behavioral baselines, calculate anomaly scores, perform peer group analysis, and detect insider threat indicators such as data exfiltration, privilege abuse, and unauthorized access patterns.

gptomics Bundle

Call germline SNPs and indels with GATK HaplotypeCaller and the GVCF joint-genotyping workflow. Covers the local-reassembly + PairHMM mechanism (why HC beats pileup callers on indels), the -ERC GVCF reference-confidence model and <NON_REF> allele, BQSR-vs-DRAGSTR and --dragen-mode error modeling, allele-specific (AS_) annotations, and edge cases (ploidy, Mutect2 mitochondria mode, sex chromosomes/PAR, contamination gating). Use when deciding whether to use HaplotypeCaller vs a pileup or DRAGEN caller, whether BQSR still earns its place, whether to call per-sample GVCFs for a cohort, or how to handle non-diploid, mitochondrial, sex-chromosome, or contaminated samples. Not for post-calling filtering depth (see variant-calling/filtering-best-practices) or cohort joint-genotyping scaling (see variant-calling/joint-calling).

gptomics Bundle

Extracts and assigns COSMIC v3.4 mutational signatures (86 SBS / 11 DBS / 18 ID / 21 CN / 16 SV) from somatic VCFs using SigProfilerSuite, MutationalPatterns, MuSiCal mvNMF, SigNet, or HRDetect. Use when characterizing DNA-damage etiology (BRCA1/2 HRD, MMR-D, POLE, APOBEC3A, UV, tobacco, aflatoxin, 5-FU/SBS17b, platinum, colibactin SBS88), routing PARP inhibitor decisions, or auditing de novo extraction vs refit choice for cohort size.

sboghossian-mini-claude-for-legal Skill

Use when instrumenting user-facing features in the legal AI product with PostHog analytics events. Defines the canonical event taxonomy, naming rules, property schemas, and anti-patterns so that all engineers emit consistent, queryable telemetry that supports product decisions, eval pipelines, and compliance audits.

sboghossian-mini-claude-for-legal Skill

Use when ingesting legal data, clause libraries, matter lists, contract schedules, or bulk templates stored in Excel (.xlsx) format into the Louis/mini-claude-for-legal data model via the Anthropic Claude API. Handles column detection, header normalization, multi-sheet parsing, and mapping of spreadsheet rows to SKILL.md or structured JSON entries, with a mandatory dry-run preview before any write. Relevant any time a law firm or legal ops team wants to migrate Excel-based legal data into the open-source skill ecosystem.

autohandai-community-skills Bundle

Performs statistical analysis of Zeek conn.log connection intervals to detect C2 beaconing patterns. Uses the ZAT library to load Zeek logs into Pandas DataFrames, calculates inter-arrival time standard deviation, and flags periodic connections with low jitter. Use when hunting for command-and-control callbacks in network data.

sboghossian-mini-claude-for-legal Skill

Use when launching a product experiment in a legal AI platform with a defined hypothesis, metric, and cohort. Guides through defining primary and guardrail metrics, calculating required sample size, creating the feature flag in PostHog or LaunchDarkly, wiring event tracking, and configuring an automatic stop-loss to revert the experiment if guardrail metrics degrade.

autohandai-community-skills Bundle

Parse Apache and Nginx access logs to detect SQL injection attempts, local file inclusion, directory traversal, web scanner fingerprints, and brute-force patterns. Uses regex-based pattern matching against OWASP attack signatures, GeoIP enrichment for source attribution, and statistical anomaly detection for request frequency and response size outliers.

autohandai-community-skills Bundle

Build network traffic baselines from NetFlow/IPFIX data using Python pandas for statistical analysis, z-score anomaly detection, and hourly/daily traffic pattern profiling

autohandai-community-skills Bundle

Tests APIs for injection vulnerabilities including SQL injection, NoSQL injection, OS command injection, LDAP injection, and Server-Side Request Forgery (SSRF) through API parameters, headers, and request bodies. The tester crafts malicious payloads targeting different backend technologies and injection contexts to extract data, execute commands, or access internal services. Maps to OWASP API8:2023 Security Misconfiguration and API7:2023 SSRF. Activates for requests involving API injection testing, SQLi in APIs, NoSQL injection, SSRF testing, or API input validation assessment.

gptomics Bundle

Detects structural variants (deletions, insertions, inversions, duplications, translocations) from Oxford Nanopore and PacBio long-read alignments with Sniffles2, cuteSV, SVIM, and assembly-based callers, joint-genotypes cohorts via the Sniffles2 .snf workflow, and benchmarks with Truvari against GIAB. Covers why an SV call is a representation artifact (the tandem-repeat BED, aligner, and Truvari params set precision/recall as much as the caller), the cuteSV per-platform parameter trap, soft-clipped supplementary alignments as the SV substrate, and the somatic/mosaic boundary to Severus/nanomonsv. Use when calling germline or somatic SVs from ONT/HiFi reads, joint-genotyping a cohort, choosing or tuning an SV caller, or benchmarking SV calls.

gptomics Bundle

Turns raw Illumina Infinium methylation BeadChip IDATs (450K, EPIC, EPICv2) into a defensible beta/M matrix with sesame (openSesame/SigDF) or minfi (RGChannelSet -> MethylSet -> GenomicRatioSet). Covers Type I vs Type II probe chemistry and why raw Type II beta is compressed, the signal-to-beta math (beta = M/(M+U+100)) and M-value logit, detection-p / pOOBAH masking including the out-of-band deletion-artifact catch, dye-bias correction, and the normalization decision (noob, funnorm, quantile, SWAN, BMIQ, dasen, sesame QCDPB). Use when reading IDATs, choosing a normalization for a 450K/EPIC/EPICv2 cohort, deciding beta vs M, masking failed probes, or producing the corrected matrix before testing. For probe/sample filtering, EPICv2 replicate collapse, and sample-identity QC see array-qc-filtering; for native long-read 5mC see long-read-sequencing/nanopore-methylation (a different platform).

sboghossian-mini-claude-for-legal Skill

Use when a user wants to generate spaced-repetition flashcards from a statute, legal code, or regulation for bar exam or legal education purposes. Produces four card formats — term/definition, article/content, fact-pattern/rule, and comparison — plus a spaced-repetition schedule. Supports export to Anki, CSV, and in-app review. Covers all jurisdictions; most heavily used for MENA statutes (UAE Labor Law, KSA Companies Law, KSA PDPL, Lebanese COC).

jmagly-ai-writing-guide Bundle

Investigate past AI session activity with cited catalog search, timelines, tool analytics, and bounded comparisons across providers

autohandai-community-skills Bundle

Automate GoPhish phishing simulation campaigns using the Python gophish library. Creates email templates with tracking pixels, configures SMTP sending profiles, builds target groups from CSV, launches campaigns, and analyzes results including open rates, click rates, and credential submission statistics for security awareness assessment.

jmagly-ai-writing-guide Skill

Build the bipartite funder↔paper analytics — per-funder paper/A-grade/mean-grade rollup, mean CD-index + novelty bias, and co-funding clusters. Runs via `aiwg corpus funder-network`.

jmagly-ai-writing-guide Skill

Show analytics and metrics from agent loop execution history

techwavedev Skill

Expert in Odoo access control: ir.model.access.csv, record rules (ir.rule), groups, and multi-company security patterns.

techwavedev Skill

Office productivity workflow covering document creation, spreadsheet automation, presentation generation, and integration with LibreOffice and Microsoft Office formats.

techwavedev Skill

Master modern business analysis with AI-powered analytics, real-time dashboards, and data-driven insights. Build comprehensive KPI frameworks, predictive models, and strategic recommendations.

autohandai-community-skills Bundle

NVIDIA DeepStream SDK 9.0 development with Python pyservicemaker API. Use when building video analytics pipelines, GStreamer-based video processing, TensorRT inference integration, object detection/tracking, or Kafka/message broker integration.

helixdevelopment Skill

Implement Extract, Transform, Load processes with best practices for data warehousing and analytics. Handle data quality, schema evolution, and performance.

techwavedev Skill

Automate Supabase database queries, table management, project administration, storage, edge functions, and SQL execution via Rube MCP (Composio). Always search tools first for current schemas.