Results for “activity”

Designs and ranks guide RNAs (sgRNAs) for CRISPR-Cas9/Cas12a gene knockout by scanning a target for PAM sites (NGG SpCas9, NNGRRT SaCas9, TTTV Cas12a, NG SpCas9-NG, near-PAMless SpRY), enumerating candidate spacers, applying hard filters (Pol-III TTTT terminator, 5' G, GC), ranking on-target activity with the context-appropriate model (Rule Set 2/Azimuth for U6/lentiviral, CRISPRscan for T7/embryo, DeepHF for high-fidelity variants, DeepCpf1 for Cas12a), and predicting the indel/frameshift outcome (Bae out-of-frame score, inDelphi, FORECasT, Lindel). Use when selecting sgRNAs to knock out a gene, choosing a nuclease/PAM for a constrained locus, picking which exon to target, or shortlisting guides before an off-target check. Off-target specificity, base/prime editing, and HDR donors are separate skills.

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Designs cytosine (CBE, C-to-T) and adenine (ABE, A-to-G) base-editor guides by positioning the target base at the activity-peak of the editing window (protospacer positions ~5-7, PAM-distal numbering), minimizing bystander edits for product purity, reading dinucleotide context (APOBEC1 TC favored / GC disfavored), and selecting the editor variant (BE4max, ABEmax, ABE8e, YE1/SECURE, TadCBE, CGBE, SpG/SpRY-BE). Covers knockout by premature stop (CRISPR-STOP/iSTOP) and splice-site disruption, the three off-target classes (Cas-dependent, Cas-independent DNA, RNA), outcome prediction (BE-Hive/DeepBE), and the base-vs-prime-vs-HDR decision. Use when installing a transition mutation without a double-strand break, knocking out a gene without indels, or choosing CBE vs ABE. Generic guide scoring, prime editing, and HDR donors are separate skills.

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Detects A/B chromatin compartments from balanced Hi-C contact matrices via eigenvector decomposition of the distance-normalized, Pearson-correlated cis matrix with cooltools (eigs_cis), then orients (phases) the compartment eigenvector against a GC or gene-density track so the active (A) sign is not arbitrary. Covers the eigenvector-is-a-choice problem (per-arm view_df to remove the centromere gradient; picking the eigenvector by max correlation with activity, not by eigenvalue), GC phasing with bioframe.frac_gc, resolution choice (100kb-1Mb), saddle plots and saddle_strength for compartmentalization strength, the cohesin-loss-strengthens-compartments result, subcompartments (SNIPER/Calder/dcHiC), and cross-condition compartment switching. Use when calling A/B compartments, computing E1/eigenvectors, phasing the eigenvector, building saddle plots, choosing a compartment resolution, quantifying compartment strength, or comparing compartmentalization across conditions.

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Nominates and assesses CRISPR off-target sites genome-wide. Enumerates candidate sites by mismatch and bulge tolerance with Cas-OFFinder/CRISPRitz, ranks them with the published CFD score (SpCas9-only, relative ranker) or MIT/CRISTA/energy models, runs variant-aware screening against gnomAD/individual genomes (CRISPRme), and frames the empirical genome-wide discovery assays (GUIDE-seq, CIRCLE-seq, CHANGE-seq, DISCOVER-seq, Digenome-seq) and high-fidelity nuclease choice (HiFi Cas9, Sniper-Cas9, eSpCas9, SpCas9-HF1). Use when assessing guide RNA specificity, choosing among candidate guides, screening a therapeutic guide against population variation, or planning empirical off-target validation. Distinguishes predicted vs detected vs validated. On-target activity scoring and deaminase (Cas-independent) base/prime-editor off-targets are separate skills.

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Queries PharmGKB / CPIC / DPWG for drug-gene interactions; calls CYP2D6/CYP2C9/CYP2C19/DPYD/TPMT/NUDT15/UGT1A1/SLCO1B1 star alleles and phenotype with PharmCAT, Cyrius (CYP2D6 structural variants), Aldy, Stargazer; applies Caudle 2020 activity-score translation. Use when implementing pharmacogenomic-guided prescribing, applying CPIC vs DPWG guidance, screening HLA risk alleles for ICI / antiepileptics / abacavir, or interpreting compound TPMT+NUDT15 thiopurine risk.

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Enumerates virtual chemical libraries via reaction SMARTS transformations using RDKit and Reaction templates, with explicit handling of atom mapping, template extraction (RDKit reaction mining), product validation, RECAP/BRICS fragmentation, R-group decomposition, matched molecular pair analysis (MMPA), and Free-Wilson analysis. Use when generating combinatorial libraries from building blocks, enumerating analog series, deriving structure-activity rules, or extracting transformations from reaction data.

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Designs novel molecules using REINVENT 4 (de novo, scaffold decoration, linker design, R-group, molecular optimization), MolMIM, Diffusion-based generators (DiGress, DiffSMol), and JT-VAE with explicit handling of multi-parameter optimization (MPO), goal-directed scoring functions, transfer/reinforcement/curriculum learning, synthetic accessibility scoring, and chemical space exploration vs exploitation. Use when designing new chemical matter against a target, decorating a scaffold, linking fragments, or optimizing a hit for multiple ADMET / activity properties simultaneously.

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Detect transcription factor binding footprints in ATAC-seq using TOBIAS, HINT-ATAC, Wellington, or scprinter. Use when identifying bound TF sites within accessible regions, correcting Tn5 insertion bias before footprinting, choosing between cleavage-based and aggregate-based footprinters, or comparing differential TF activity between conditions.

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Use when building content-heavy sites with Astro, deciding between SSG/SSR/hybrid, choosing client directives (idle/visible/load/media), structuring content collections with type-safe schemas, integrating React/Vue/Solid/Svelte components in the same project, or migrating from Next.js for marketing/docs. Triggers: client:idle vs client:load tradeoffs, content collections schema with zod, image optimization via @astrojs/image, view transitions, server islands, MDX layouts. NOT for SPA-style apps that need full interactivity (use Next/Remix), Astro internals/plugin authoring, or non-content sites where islands provide no benefit.

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Automate Amplitude tasks via Rube MCP (Composio): events, user activity, cohorts, user identification. Always search tools first for current schemas.

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AI-assisted label triage for NVIDIA/NemoClaw issues and PRs. Reads triage-instructions.md at runtime for consistent label guidance. Supports single-item mode (give it a number) and batch mode (fetches up to 50 unlabeled open items). On approval, applies labels and an optional triage comment via gh CLI, then logs the session to the daily-rhythm activity folder. Trigger keywords - triage, label issues, suggest labels, batch triage, triage issue, triage PR, label this, what labels.

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Use this skill when building analytics dashboards with nuxt-ui-tools as a package consumer. Covers schema and view functions (defineDashboardSchema, defineDashboardView) that take their context as typed params, useDashboard with a getter that rebuilds on input change, typed injection (useDashboardView, injectDashboard, InferDashboard, InferDashboardView), filters declared inline with the f builder and synced with the URL, memory, or an external store (one value per key across views), headless filters, filter controls and the shipped UI (UiDashboardPage, UiDashboardFilters, UiDashboardFilter, UiDashboardViewTabs) with slot overrides, remote paginated pickers and remoteTableOptions, staged queries (essential / background / deferred) with select and dependent requires, lazy enabled conditions on views, queries, and filters (blocks of disabled queries hidden, grids closing up), derived values, views (tabs), query-scoped filters, number formats (presets, Intl options, useDashboardFormat), and the dashboard blocks (stats with trends, goals, and comparisons, stat groups, gauges, unovis charts with highlights, value labels, and totals, lists with progress rings, bars, funnel, alerts, activity feeds, sortable tables, custom widgets) with their automatic loading, error, empty, and refresh states, card menus, header and footer actions, row actions, drill-down and selected state, card tabs, split cards, comparison periods, auto-refresh, and data freshness.

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Automate Amplitude tasks via Rube MCP (Composio): events, user activity, cohorts, user identification. Always search tools first for current schemas.

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Track TikTok ad activity and monitor advertiser changes using PipiAds tools for TikTok ad discovery and Facebook-based monitoring workflows.

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Monitor Power Automate flow health, track failure rates, and inventory tenant assets using the FlowStudio MCP cached store. The live API only returns top-level run status. Store tools surface aggregated stats, per-run failure details with remediation hints, maker activity, and Power Apps inventory — all from a fast cache with no rate-limit pressure on the PA API. Load this skill when asked to: check flow health, find failing flows, get failure rates, review error trends, list all flows with monitoring enabled, check who built a flow, find inactive makers, inventory Power Apps, see environment or connection counts, get a flow summary, or any tenant-wide health overview. Requires a FlowStudio for Teams or MCP Pro+ subscription — see https://mcp.flowstudio.app

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Detects insider data exfiltration by analyzing DLP policy violations, file access patterns, upload volume anomalies, and off-hours activity in endpoint and cloud logs. Uses pandas for behavioral analytics and statistical baselines. Use when investigating insider threats or building user behavior analytics for data loss prevention.

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Detects early-stage ransomware indicators in network traffic before encryption begins, including initial access broker activity, command-and-control beaconing, credential harvesting, reconnaissance scanning, and staging behavior. Uses network detection tools (Zeek, Suricata, Arkime), SIEM correlation rules, and threat intelligence feeds to identify ransomware precursor patterns such as Cobalt Strike beacons, Mimikatz network signatures, and RDP brute-force attempts. Activates for requests involving pre-ransomware detection, network-based ransomware indicators, or early warning ransomware monitoring.

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Configures Fail2ban with custom filters and actions to detect port scanning activity, SSH brute force attempts, and network reconnaissance, automatically banning offending IP addresses and alerting security teams to suspicious network probing.

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Detect lateral movement in network traffic using Zeek (formerly Bro) log analysis. Parses conn.log, smb_mapping.log, smb_files.log, dce_rpc.log, kerberos.log, and ntlm.log to identify SMB file transfers, NTLM account spray activity, remote service execution, and anomalous internal connections.

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Detect network reconnaissance and port scanning using Suricata and Snort IDS signatures, threshold-based detection rules, and traffic anomaly analysis to identify Nmap, Masscan, and custom scanning activity.

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Detects defense evasion techniques used by adversaries in endpoint logs including log tampering, timestomping, process injection, and security tool disabling. Use when investigating suspicious endpoint behavior, building detection rules for evasion tactics, or conducting threat hunting for stealthy adversary activity. Activates for requests involving evasion detection, defense evasion analysis, log tampering detection, or MITRE ATT&CK TA0005.

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Detect insider threat behavioral indicators including unusual data access, off-hours activity, mass file downloads, privilege abuse, and resignation-correlated data theft.

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Detects rootkit presence on compromised systems by identifying hidden processes, hooked system calls, modified kernel structures, hidden files, and covert network connections using memory forensics, cross-view detection, and integrity checking techniques. Activates for requests involving rootkit detection, hidden process discovery, kernel integrity checking, or system call hook analysis.

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Deploys canary files (honeytokens) across file systems to detect ransomware encryption activity in real time. Uses strategically placed decoy documents monitored via file integrity monitoring or OS-level watchdogs to trigger alerts when ransomware modifies or encrypts them. Activates for requests involving ransomware canary deployment, honeyfile setup, deception-based ransomware detection, or file integrity monitoring for encryption.

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