7,241 件 ・ 関連度順
概要と使いどころ
Use when targeting Communications Earth & Environment or deciding whether an earth, environmental, or planetary-science manuscript fits this venue. Encodes the journal's fit, the solid-and-complete-advance bar, Nature Portfolio reporting/data standards, house style, official-submission re-check, and desk-reject heuristics.
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Use when preparing ACM CCS appendices and supplementary material, including the ethics considerations appendix, protocol transcripts, formal proofs, measurement tables, and anonymized supporting material under the 12-page body limit, anonymity, and reviewer-discretion constraints for a security paper.
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Use when organizing the ACM MM (ACM Multimedia) supplementary material due after the paper deadline — deciding what belongs in the 6-8 page body versus the supplement, packaging video/audio/interactive demos that render on a reviewer's machine, keeping all assets anonymous for double-blind tracks, and pointing to code and data.
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Use when organizing appendices and supplementary material for an ACL paper under ACL Rolling Review, covering the mandatory Limitations and optional ethics sections, appendices after references, anonymized software and data archives, the no-cloud-links rule, and deciding what must stay in the 8-page or 4-page body.
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Use when preparing AAMAS supplementary material - proofs, extended game and mechanism definitions, extra multiagent experiments, opponent-set details, and the anonymized artifact zip - under the size cap, anonymity, and reviewer-discretion limits, including how to split a game-theory-plus-experiments paper across the 8-page body and the supplement.
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Use when organizing AAAI supplementary material, including the technical appendix, multimedia appendix, and code/data ZIPs, while respecting that AAAI supplements are due with the paper, treated as immutable after submission, must stay double-blind, and should never hide main-paper-critical evidence from reviewers who skim the appendix.
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Build a prospect list of companies with decision makers, verified contact info, and hiring/intent signals. Use when asked to find leads by industry, build an account list with specific titles, prospect companies that are actively hiring, or create a targeted outreach list filtered by company size, location, and hiring activity.
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For founders who don't know where to start with paid ads. Analyzes ICP, competitor ad presence, budget constraints, and product type to recommend which 1-2 paid channels to start with and provides a 90-day ramp plan. Prevents the common mistake of spreading a small budget across too many platforms.
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Configure a Simulink model for Simulink Real-Time code generation and deployment. Use when setting up a model for Simulink Real-Time, selecting the correct system target file, fixing TLC/STF mismatches, applying fixed-step solver settings, validating target-platform compatibility, or configuring Simulink Real-Time build options before model build.
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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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Visualises RNA-modification data with transcript-feature metagene plots (Guitar GuitarPlot; MetaPlotR; deepTools computeMatrix scale-regions), peak-centred heatmaps (ComplexHeatmap; deepTools plotHeatmap), IP-vs-input paired browser tracks (log2 IP/input bigWig via deepTools bamCompare; pyGenomeTracks; Gviz; IGV/UCSC track hubs), DRACH sequence-logo plots (ggseqlogo; MEME), feature-distribution stacked bars, and volcano/MA plots for differential modification. Establishes stop-codon enrichment in the metagene plot as the biological QC anchor for any MeRIP dataset (Dominissini 2012; Meyer 2012). Use when producing the canonical metagene plot with stop-codon enrichment as a QC anchor, building paired IP/input genome-browser tracks at single-locus resolution, plotting peak-centred heatmaps clustered by condition, summarising peak distribution across transcript features, generating DRACH motif logos as sanity checks, rendering volcano plots of differential m6A, or reproducing the stop-codon enrichment plot.
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Estimates the minimum biological replicates (or cells/events) for a target power at a target FDR in genomics experiments using ssizeRNA, PROPER, powsimR for scRNA-seq, and pilot-data dispersion estimation from DESeq2/edgeR. Covers the biological-versus-technical replication distinction (technical replicates do not add degrees of freedom for biological inference), replicate-number-versus-sequencing-depth budgeting, scRNA-seq sample-versus-cell allocation under a pseudobulk model, and the critique that "n=3" is a publication convention rather than a power calculation. Use when budgeting a sequencing experiment, writing the sample-size justification in a grant, estimating replicates from pilot data, allocating a fixed budget between samples and depth, or planning scRNA-seq cohort size. For clinical-trial sample size see clinical-biostatistics/power-and-sample-size; for the power-given-n direction see experimental-design/power-analysis.
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Designs pooled sgRNA libraries for CRISPR knockout, interference (CRISPRi), activation (CRISPRa), Cas12a multiplex, base-editor, and prime-editor screens. Covers on-target scoring (Rule Set 2, Azimuth, DeepSpCas9, CRISPRon), off-target scoring (CFD, MIT), TSS-relative positioning for CRISPRi/a (Horlbeck, Dolcetto, Calabrese), PAM-variant chemistries, control-guide composition, oligo cloning architecture, and library QC. Use when choosing a genome-wide library (GeCKOv2 vs Avana vs Brunello vs TKOv3 vs Inzolia), designing a focused or paralog-focused custom library, picking CRISPRi vs CRISPRa TSS windows, deciding control-guide proportions, or diagnosing library skew and dropout in a freshly cloned pool.
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Designs and analyzes in vivo CRISPR screens in animal tumor models, organoids, and immune-cell adoptive transfers. Covers bottleneck math (250x cells/sgRNA requires ~25M cells implanted; impossible for most syngeneic models, forcing focused libraries), focused library design (Manguso 2017 Nature 547:413 immune screen; Chen 2015 tumor screens), CRISPR-StAR intrinsic-control screening (Uijttewaal 2025 Nat Biotechnol 43:1848), clonal-dynamics-limited detection, tumor-explant DNA recovery, syngeneic vs xenograft vs PDX considerations, and the relationship to downstream MAGeCK / drugZ analysis. Use when designing in vivo CRISPR screens for tumor / immune / metastasis biology, choosing focused vs genome-wide for animal models, addressing bottleneck-induced clonal collapse, picking the syngeneic / xenograft / PDX model, integrating in vivo with in vitro results, or applying CRISPR-StAR for animal experiments.
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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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Align preprocessed CLIP-seq reads (eCLIP, iCLIP, iCLIP2, PAR-CLIP) to genome with STAR or bowtie2 using crosslink-preserving parameters, choosing between unique-mapper-only and multi-mapper-aware alignment for repeat-binding RBPs, deciding STAR vs HISAT2 memory trade-offs, and applying ENCODE-compatible filters. Use when turning preprocessed CLIP FASTQ into a deduplicated, MAPQ-filtered BAM ready for peak calling or crosslink-site detection.
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Identifies essential genes from CRISPR-Cas9 fitness screens using BAGEL2 (Kim & Hart 2021 Genome Med), a Bayesian classifier scoring per-gene Bayes Factors via log-likelihood ratios over per-sgRNA fold changes, calibrated against CEGv2 core-essentials (Hart 2017 G3, ~684 genes) and NEGv1 non-essentials (Hart 2014, ~927 genes). Covers the fc + bf + pr workflow, the linear-extrapolation improvement over BAGEL1 truncation, multi-target off-target correction, tumor-suppressor sensitivity (BAGEL2 detects enrichment), and BF calibration (BF >6 ≈ 90% posterior per Hart 2017; ~5% FDR by BAGEL convention). Use when classifying essential vs non-essential genes, calibrating BAGEL2 thresholds against PR curves, identifying tumor suppressors alongside essentials, comparing BAGEL2 hits to MAGeCK / drugZ, or generating publication-quality essentiality calls.
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Quantifies CRISPR editing outcomes with CRISPResso2 (Clement 2019 Nat Biotechnol) across Cas9-nuclease (indels, HDR), CBE and ABE base editors (target conversion + bystander), and prime editor (pegRNA-templated) modes. Covers single-amplicon (CRISPResso), multi-sample batch (CRISPRessoBatch), pooled-amplicon (CRISPRessoPooled), WGS off-target (CRISPRessoWGS), and sample-comparison (CRISPRessoCompare) workflows; quantification-window math that controls what is called edited; substitution-vs-indel diagnostic to distinguish BE from Cas9 contamination; MMEJ deletion pattern interpretation; allele-frequency tables; and failure modes from amplicon misalignment or contamination. Use when quantifying editing from amplicon sequencing, choosing CRISPResso mode by design, distinguishing intended edits from bystanders and indel byproducts, debugging low-alignment runs, or generating publication-grade editing reports.
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Designs covalent inhibitors and warheads targeting cysteine, lysine, serine, threonine, tyrosine, and aspartate residues, with explicit handling of warhead reactivity (acrylamide, chloroacetamide, vinyl sulfone, sulfonyl fluoride, fluorosulfate, aldehyde, boronate, nitrile), reversibility (kinact/Ki, t_residence), glutathione (GSH) stability, intrinsic reactivity assays, and covalent docking (DOCKovalent, GOLD, HCovDock). Use when designing covalent inhibitors for targeted covalent inhibition (TCI), KRAS G12C-style approaches, or rationalizing covalent SAR.
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Predict enhancer-gene regulatory connections from ATAC-seq using ABC, ENCODE-rE2G, HiChIP, or Cicero. Use when linking distal enhancers to target genes, choosing between contact-aware (ABC, ENCODE-rE2G), accessibility-only (Cicero), and orthogonal (HiChIP H3K27ac, EpiMap) approaches, validating predictions against CRISPRi-FlowFISH gold-standard, or building cell-type-specific regulatory maps for fine-mapping or therapeutic target discovery.
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Create a reusable SkillPack from a successful completed task. Use when the user wants to convert a one-off research, coding, analysis, or content workflow into a distributable local SkillPack with `skillpack.json`, local skills under `skills/`, starter prompts, start scripts, and an optional zip package.
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Guide a brand-new SearchCLI/vs user from first-time usage questions to sign-up, purchase of Viking AI Search, AK/SK setup, and a working authenticated CLI. Use when the user says they downloaded or installed SearchCLI/vs and asks how to use it, how to start, sign up, buy, or onboard.
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Drives a multi-turn conversation with a LiveKit agent running locally to see what it does. Use when the user says "test my agent", "try my agent", "does this work", "why did it call that tool", "it says the wrong thing when I ask X", "test this change", or whenever you have edited an agent and need to check how it behaves. Wraps `lk agent debugger`: start the agent in text mode, send turns, read the tool calls, handoffs, errors and logs behind each reply, and restart after an edit. It runs without audio or a LiveKit room at one LLM call per turn, so it is the preferred way for a coding agent to live-test during development, and the default when the user says "test" without naming unit tests or simulations.
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Translate NI-DAQmx C function signatures into correct calldaqlib MATLAB calls. Use when the user mentions calldaqlib, any DAQmx* C function name (DAQmxCfgSampClkTiming, DAQmxExportSignal, DAQmxSetStartTrigRetriggerable, DAQmxGetSampClkRate, etc.), or needs NI-DAQmx functionality not exposed by the daq object. Covers: projection rules (taskHandle implicit, output pointers become return values, buffer-size args, enum-as-string), multi-task semantics, start() clobber, device-level empty-daq workaround, dictionary returns, string getter placeholder, array getter placeholder. Trigger contexts: low-level DAQ, escape hatch, retriggerable acquisition, shared timebase, export signal, connect terminals, external sample clock, trigger configuration, NI driver, C function translation.
日本語の概要は準備中です。原文の説明を表示しています。