Results for “sequences”

Query the UCSC Genome Browser REST API to retrieve regulatory tracks, DNA sequences, cCRE annotations, TF binding clusters, and track schemas for any genomic region. Use when the user wants to look up what regulatory elements exist at a genomic locus, retrieve DNA sequence under peaks, query ENCODE cCREs or TF rPeak clusters from UCSC, check what tracks are available for a genome assembly, get chromatin accessibility across cell types, or cross-reference ENCODE data with UCSC-hosted annotations. Also use when the user mentions UCSC, genome browser, cCRE lookup, SCREEN, TF binding clusters, DNA sequence retrieval, or track data extraction.

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ครูสอนโยคะ — Hatha/Vinyasa/Yin sequences + asana ละเอียด + breathing + modification + prop use สำหรับ practitioner ทุกระดับ

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Assemble a finished piece from human-written fragments via an orchestrated two-loop pipeline - an assembly loop (assembler + cold reviewer) that sequences the fragments into a draft, then a polish loop (polisher + cold reviewer), then frequency analysis and a catalog-deslop pass with a regression gate. Two modes with opposite fidelity contracts - stitch mode preserves the author's exact wording, narrative mode preserves every idea but may rewrite freely. Use when the user says "mosaic", "assemble my fragments", "stitch these notes into a post", or provides a fragments file to turn into a finished piece. For writing from a topic with research, use article-factory; for prose from scratch, use the prose skill.

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Outbound SDR (Sales Development Representative) operating system that runs the full top-of-funnel motion across HubSpot (CRM, engagement, and source of truth) and Exa (web research + signals). Use this skill WHENEVER the user is doing outbound sales development, building target/prospect lists, defining or refining an ICP, enriching leads, researching accounts or people before outreach, writing cold emails or multi-touch sequences, qualifying or scoring leads, logging activity to CRM, handing meetings off to AEs, or reporting on pipeline. Trigger it even when the user only says things like "find me 50 leads", "research this account", "write a cold email to this person", "score these leads", "log this in HubSpot", or "build a sequence"; these are all SDR tasks this skill governs. Do not wait for the user to say "SDR" or "prospecting" explicitly.

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Rigorous analysis expert covering limits, continuity, sequences, series, and measure theory foundations

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Comprehensive calculus expert covering limits, derivatives, integrals, sequences, series, and multivariable calculus with rigorous proofs and practical applications

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Use this skill when designing, building, or troubleshooting FSC Action Plan templates for client-facing task sequences such as client onboarding, account opening, annual review preparation, and compliance tasks. Trigger keywords: Action Plan template, ActionPlanTemplate, ActionPlan object, FSC task sequence, onboarding checklist, review prep tasks. NOT for designing the onboarding process itself — use admin/client-onboarding-design. NOT for Health Cloud care plan templates — use admin/care-plan-configuration.

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Configuring or troubleshooting Salesforce CPQ Advanced Approvals: SBAA__ApprovalRule__c, SBAA__ApprovalVariable__c for cross-line aggregation, SBAA__ApprovalChain__c for ordered approver sequences, escalation timeouts, Smart Approvals for re-quote skip logic, and the managed package's permission sets. Trigger keywords: CPQ Advanced Approvals, SBAA approval rule, approval variable, approval chain, discount approval, line-level approval, Smart Approvals, requote approval. NOT for standard non-CPQ Salesforce approval processes - use admin/approval-processes. NOT for CPQ price rules and discount schedules - use admin/cpq-pricing-rules.

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Set up customer outreach sequences via [Lemlist](https://composio.dev/toolkits/lemlist), [Reply.io](https://composio.dev/toolkits/reply-io), or [Woodpecker](https://composio.dev/toolkits/woodpecker-co)

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Use Mermaid diagrams in DecisionsAI to explain technical topics — architecture, flows, sequences, and data models via the freestanding diagram viewer.

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Multi-channel ABM automation that turns LinkedIn URLs into coordinated outbound campaigns. Scrapes profiles, enriches with Apollo (email + phone), gets mailing addresses via Skip Trace, then orchestrates email sequences, LinkedIn touches, and handwritten letters via Scribeless. The secret weapon for standing out in crowded inboxes.

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Auto-assembles a domain-specific expert panel (7–10 experts), scores any content or strategy artifact against a typed rubric, and iterates until the aggregate hits 90+ (max 3 rounds). Use as a quality gate on copy, email sequences, landing-page drafts, strategy docs, charts, titles, or recruiting evaluations — or when another skill needs a final review gate on its output. Triggers on "expert panel this", "score this", "rate these variants", "quality check this", "panel review", "expert score", "evaluate this copy/strategy/page". For variant generation and multi-round conversion optimization see autoresearch; for live-URL CRO auditing see conversion-ops; for the scripted content-production pipeline see content-pipeline.

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Run Karpathy-style autoresearch optimization on any content. Generates 50+ variants, scores with a 5-expert simulated panel, evolves winners through multiple rounds, outputs optimized version + full experiment log. Use when optimizing landing pages, email sequences, ad copy, headlines, form pages, CTA text, or any conversion-focused content. Triggers on "optimize this page", "run autoresearch", "score these variants", "A/B test this copy".

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Apply normative BDI reasoning to agents that must detect norms, choose which commitments to internalize, and resolve conflicts by comparing consequences. Use when obligations, prohibitions, or policies collide in autonomous systems. NOT for simple fixed-priority rules, pure constraint satisfaction, or domains where no real normative conflict exists.

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Council — 5 independent AI perspectives + mutual critique + synthesis (adapted from karpathy/llm-council for Claude Code). For high-stakes decisions where the answer does NOT follow unambiguously from the data — go/no-go before real consequences, critiquing a methodology, choosing between competing approaches, pressure-testing a conclusion you're attached to, designing risk controls. NOT for log/data analysis (the council has no data access) and not for factual lookups. Triggers — "convene the council", "run it past the council", "go/no-go", "pressure-test this".

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Assigns pathogen lineages (SARS-CoV-2 Pangolin UShER mode; Nextclade clade + QC; pango-designation alias resolution) and tracks variant frequencies over time using Nextstrain (Augur + Auspice), wastewater deconvolution (Freyja, COJAC, alcov, lineagespot), lineage-fitness modelling (multinomial logistic), and recombinant detection (3SEQ, RDP4, Bolotie). Covers Pangolin pangolin-data and Nextclade dataset version pinning (mandatory; lineage-defining mutations change with dataset), Freyja barcode forward-only date constraint, ARTIC primer scheme churn (V3/V4/V4.1/V5.3.2/Midnight) with dropout regions, and recombinant X-prefix designation lag. Use when assigning Pango lineages and Nextclade clades to viral consensus sequences, building Nextstrain Augur surveillance pipelines, deconvolving wastewater into lineage frequencies with Freyja, tracking lineage frequencies over time, handling ARTIC primer dropouts, or running surveillance for SARS-CoV-2/influenza/Mpox/RSV/H5N1/measles.

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Calculates statistical power for high-dimensional genomics experiments (bulk RNA-seq, scRNA-seq, ATAC-seq, ChIP-seq, methylation, proteomics) under negative-binomial count models using RNASeqPower, PROPER, and simulation via powsimR, distinguishing per-gene from marginal (transcriptome-wide) power, the role of mean expression and dispersion, and the sequencing-depth-versus-replicate tradeoff. Covers simulation as the honest default for overdispersed counts, FDR-aware average power versus single-test power, observed/post-hoc power as an anti-pattern, and the winner's-curse / Type-S / Type-M consequences of underpowering. Use when planning replicate number for a sequencing experiment, deciding whether to add depth or samples, choosing closed-form versus simulation power, estimating power from pilot dispersions, or justifying replication in a grant. For clinical-trial power see clinical-biostatistics/power-and-sample-size; for the inverse sample-size question see experimental-design/sample-size.

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Retrieve records from NCBI databases using Biopython Bio.Entrez (EFetch, ESummary). Use when downloading sequences, fetching GenBank/GenPept records, getting document summaries, parsing nested XML, navigating GI deprecation, choosing between rettype+retmode combinations, and parsing into Biopython SeqRecord/SwissProt objects. Covers nucleotide, protein, gene, pubmed, sra, gds, taxonomy, snp, clinvar.

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Reconstruct ancestral states at internal phylogenetic nodes for sequences (PAML codeml, IQ-TREE --ancestral, GRASP, FastML), discrete traits (corHMM hidden-rate Markov, ape::ace, phytools::make.simmap stochastic mapping, BayesTraits), and continuous traits (phytools::fastAnc, geiger Brownian/OU, RPANDA). Use when designing constructs for ancestral protein resurrection, tracing trait evolution along a tree, performing stochastic character mapping, testing models of trait evolution (BM vs OU vs EB), inferring ancestral genome content via Dollo or DTL reconciliation, or quantifying ancestral-state uncertainty for downstream comparative analyses.

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Analyze codon usage and calculate CAI (Codon Adaptation Index), RSCU, and Nc with Biopython, and produce naive max-CAI codon-optimized sequences. Use when scoring a gene's codon bias against a host, optimizing a CDS for heterologous expression, or studying synonymous codon selection.

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Run remote BLAST searches against NCBI servers using Biopython Bio.Blast.NCBIWWW. Use when identifying unknown sequences, finding homologs, picking the correct BLAST program (blastn/blastp/blastx/tblastn/tblastx/psiblast/megablast/dc-megablast), interpreting Karlin-Altschul E-values, avoiding the max_target_seqs trap (Shah 2019), choosing composition-based statistics, or limiting searches by organism. Covers RID lifecycle, database choice (nt/nr/refseq_select/swissprot), word-size and CBS taxonomy.

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Discovers de novo motifs and tests known motif enrichment in ChIP-seq, ATAC-seq, or other peak sequences using HOMER, MEME-ChIP (STREME, CentriMo, TOMTOM, FIMO), monaLisa, and AME. Handles background selection (GC-matched, dinucleotide-shuffled, Markov order-2, peak-flanks), motif databases (JASPAR 2024 CORE PWMs, JASPAR 2026 deep-learning collection, HOCOMOCO v12, HOMER built-in), centrally-enriched motif testing, and differential motif analysis. Use when identifying TF binding motifs in peaks, testing for known TF enrichment, scanning for motif instances, comparing motif content between conditions, or interpreting motifs from deep learning models.

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Download large datasets from NCBI efficiently using EPost, history server, batching, rate limiting, and retry logic. Use when bulk-fetching tens of thousands of sequences, pulling all results of a large ESearch, designing reproducible pipelines, comparing E-utilities to NCBI Datasets v2 CLI, or implementing checksum-validated downloads. Encodes WebEnv TTL (~8h), EPost 200-ID limit, retmax caps, parallelization design, and integrity verification.

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Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm selection based on dataset size, sequence divergence, and downstream application. Use when aligning three or more homologous sequences for phylogenetics, conservation analysis, or evolutionary studies.

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