Detect somatic and germline copy number variants from targeted, exome, and whole-genome sequencing with CNVkit, a read-depth caller that combines on-target and off-target (antitarget) coverage. Covers panel-of-normals construction, flat-reference tumor-only calling, hybrid/amplicon/WGS modes, CBS vs HMM segmentation selection, purity-aware integer calling, and reconciliation against GATK and allele-specific callers. Use when calling CNVs from hybrid-capture panels or exomes, deciding whether CNVkit (depth-only) is the right tool versus an allele-specific caller, building a panel of normals, diagnosing flat-reference false positives, or interpreting log2 ratios into copy-number states.
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 thresholds, comparing replicates with IDR rescue and self-consistency ratios, or distinguishing failed IP from over-amplified library.
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 callers for the same RBP.
Create, manipulate, and convert bedGraph files for genome browser visualization. Covers bedGraph format, conversion to/from bigWig, normalization, and signal processing. Use when handling coverage and signal tracks from ChIP-seq, ATAC-seq, or RNA-seq.
ATAC-seq library quality control -- TSS enrichment, FRiP, fragment-size periodicity, library complexity (NRF/PBC1/PBC2), mitochondrial fraction, and ENCODE 4 thresholds. Use when assessing whether an ATAC-seq library passes ENCODE acceptance criteria, diagnosing transposition artefacts, comparing Omni-ATAC vs standard prep quality, or selecting which replicates to drop before peak calling.
Run Bayesian phylogenetic analysis with MrBayes, BEAST2, RevBayes, and PhyloBayes including MCMC convergence diagnostics and model comparison. Use when needing posterior probability support, Bayesian model averaging, site-heterogeneous models for deep phylogenies, or formal model comparison via stepping-stone sampling.
Research startups and emerging companies with funding data, team composition, product positioning, market traction, and news coverage. Combines Apollo firmographics, LinkedIn team data, and web intelligence for comprehensive startup due diligence.
Portable multi-source research with cross-source validation and an offline evidence ledger. Use for fact-checking, comprehensive research, or any question requiring multiple independent perspectives; work with the host agent's search tools and optionally add SandBase Tavily, Exa, Scholar, and Cloudsway coverage.
Research podcasts, episodes, and audio content by searching YouTube (where most podcasts crosspost), web sources, and transcript databases. Discover relevant shows, track guest appearances, and analyze topic coverage in the podcast ecosystem.
Track media coverage, press mentions, journalist activity, and industry narrative across news outlets, Twitter, and LinkedIn. Ideal for PR teams monitoring earned media, tracking campaign impact, and identifying journalist relationships.
Aggregate news from Google News, Tavily, and Exa to get comprehensive coverage of any topic. Cross-references multiple news sources, identifies publication velocity, detects emerging stories, and provides citation-ready news intelligence.
Monitor brand mentions, sentiment, and reputation across Twitter, Reddit, news, and social platforms through SandBase. Use when asked for brand monitoring, reputation tracking, social listening, PR coverage analysis, or competitive brand intelligence.
Map any industry's competitive landscape using company databases, academic research, news coverage, LinkedIn activity, and job market signals. Produces industry overviews with key players, market segments, growth indicators, and emerging disruptors.
Track real-time events, announcements, and breaking developments across Twitter, Reddit, news outlets, and web search. Monitors event progression, public reaction, key moments, and aftermath coverage for crisis response and opportunity detection.
Search and monitor news articles across Google News through SandBase. Use when asked for news monitoring, current events research, news coverage analysis, or media tracking.
Create a 30/60/90-day cash-flow forecast from AR, AP, opening cash, payment timing, and fixed-cost data. Use when asked about runway, payroll coverage, liquidity risks, or a near-term cash crunch.
Analyze competitor content coverage and uncover differentiated content opportunities using web search, page extraction, and DataForSEO content analysis. Use when asked for competitor content research, editorial gap analysis, content brief inputs, or topic whitespace.
Build a knowledge base from web content with Firecrawl. Use for local reference docs, RAG-ready chunks, fine-tuning datasets, documentation mirrors, topic corpora, or LLM-ready markdown organized from web sources.
Use when working on Formax code changes and you need a disciplined dev loop: keep a single mainline task, avoid scope drift, run only targeted tests (no coverage), avoid partial staging (MM), run mandatory review before commit, include an incremental optimization check, and keep commits small and reviewable.
Use when implementing features or fixing bugs with strict Test-Driven Development (TDD). Activate for coding tasks that require new functionality, refactoring, or comprehensive test coverage, especially when the user mentions TDD or Test Driven Development.