「eq」の検索結果

Write, open and — when allowed — merge a pull request for the current feature branch of a {{engine_name}} project, with or without a plan. Builds a plain-language PR text (one feature per line) from the plan's `## Modules` and task `WHY:` lines, or — without a plan — from the commits and the code changes themselves; pushes the current state (asking where to end when it stands inside a plan module), opens or updates the branch's single open PR through the GitHub MCP, and merges with a merge commit only when the merge brings nothing from the base branch. Levels: remind (text only), create, merge; capped by `git.pull_requests.max_level`. Trigger phrases: "pull request", "open a PR", "create PR", "PR description", "merge the PR". For commit messages use /unikit-commit; for reviewing a PR's code use /unikit-review.

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Routes LLM requests to a local model first (Ollama, LM Studio, llamafile), validates the response quality, and escalates to cloud only when the local result fails. Tracks local vs escalated vs cloud outcomes in a persistent dashboard. Use when: (1) user asks to run a task with a local model first, (2) user wants to reduce cloud API costs or keep requests private, (3) user wants post-outcome quality validation before committing to a local result, (4) user asks to see token savings or the routing dashboard, (5) any request where local-vs-cloud routing should be decided automatically with a quality gate. Supports Ollama, LM Studio, and llamafile as local providers.

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Use this skill when users need to search academic papers, download research documents, extract citations, or gather scholarly information. Triggers include: requests to "find papers on", "search research about", "download academic articles", "get citations for", or any request involving academic databases like arXiv, PubMed, Semantic Scholar, or Google Scholar. Also use for literature reviews, bibliography generation, and research discovery. Requires OpenClawCLI installation from clawhub.ai.

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Operate Aavegotchi Gotchiverse player workflows on Base mainnet (8453): alchemica channeling, surveying and harvesting, crafting installations/tiles, building on parcels (equip/unequip/move/batch equip), installation upgrades, craft/upgrade queue management, and parcel access-right management. Use when interacting with Realm/Installation/Tile diamonds via subgraph-first discovery and onchain verification/execution with Foundry cast.

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Babysit a GitHub pull request after creation by continuously polling review comments, CI checks/workflow runs, and mergeability state until the PR is merged/closed or user help is required. Diagnose failures, retry likely flaky failures up to 3 times, auto-fix/push branch-related issues when appropriate, and keep watching open PRs so fresh review feedback is surfaced promptly. Use when the user asks Codex to monitor a PR, watch CI, handle review comments, or keep an eye on failures and feedback on an open PR.

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Use OpenClaw's exec tool to inspect orgs, sources, and run bounded read-only SQL through the OneQuery CLI directly.

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。

Update the title and body of one or more pull requests.

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Clarify ambiguous requirements through focused dialogue before implementation. Use when requirements are unclear, features are complex (>2 days), or involve cross-team coordination. Ask two core questions - Why? (YAGNI check) and Simpler? (KISS check) - to ensure clarity before coding.

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Digital equity and trauma-informed design for marginalized populations. Activate on "accessibility", "offline-first", "trauma-informed", "reentry", "recovery population", "shared device", "unstable phone", "digital equity", "design justice", "low-literacy", "intermittent access". NOT for general UX, marketing optimization, or enterprise SaaS design.

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Prepare and publish upstream issues, feature requests, discussions, pull or merge requests, and patch submissions in the channel the canonical project expects. Use when reporting a problem upstream, requesting a feature, contributing a change, or asking to submit upstream.

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Generates a pull request description for the current branch and writes it as Markdown to .git/magit/posts/new-pullreq for magit-forge. Use when the user asks for a PR description, PR summary, or write-up of what a branch changes, or is preparing to open a pull request.

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Checks the canonical upstream issue tracker, discussion forums, and open pull requests, merge requests, or equivalent change queues for existing reports, discussion, or work on a problem just discussed. Use before diagnosing, fixing, or reporting an apparent open-source problem to avoid duplicate effort and missed context.

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Redacta un pull request para la rama actual rellenando la plantilla de PR del repositorio en función de los cambios de la rama. Úsalo cuando la persona pida abrir/crear un PR, preparar un pull request o escribir la descripción de un PR (p. ej. "abre un PR", "redacta el pull request de esta rama"). No hace merge.

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Identifies differential m6A methylation between conditions from MeRIP-seq paired IP/input data using exomePeak2 (GC-bias-aware differential via its bam_ip/bam_input control + bam_treated_ip/bam_treated_input treatment arms), QNB beta-binomial, MeTDiff HMM, and RADAR, plus the paired-symmetric edgeR/DESeq2-on-peak-counts route when batch/lot covariates need fixed-effect handling that exomePeak2's API does not accept. Covers paired vs unpaired vs interaction designs, batch confounding and per-lot meta-analysis, the stoichiometry-vs-expression-vs-IP-efficiency confound, and effect-size filtering against under-powered N=2 designs. Use when comparing m6A across two or more conditions, choosing between exomePeak2/QNB/RADAR/MeTDiff for a design, handling batch confounding when exomePeak2's API is too rigid, distinguishing real hyper/hypo-methylation from expression shifts, applying effect-size thresholds, or planning orthogonal stoichiometry validation (GLORI/SAC-seq/m6Anet mod_ratio).

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Designs genomics experiments so technical nuisance variation (batch, lane, plate, flow cell, operator, reagent lot, processing day) is balanced against the biological variable of interest and therefore estimable rather than confounded, using constrained sample-to-batch assignment (designit, OSAT), the confounder/mediator/collider distinction, and the principle that no post-hoc correction recovers a fully confounded design. Covers detecting hidden batches with surrogate variable analysis, a decision table for downstream correction (ComBat-seq, RUVSeq, SVA) whose execution is deferred to differential-expression/batch-correction, and reproducibility metadata. Use when assigning samples to sequencing batches/lanes/plates, avoiding batch-condition confounding, deciding whether a design is salvageable by correction, choosing a correction method, or estimating the number of hidden batches. For the experimental unit, randomization, and blocking concepts see experimental-design/randomization-blocking.

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Build volcano and MA plots from differential-expression / association results with LFC shrinkage, FDR-adjusted thresholds, sensible label placement, and axis-truncation conventions. Covers EnhancedVolcano, ggplot2, matplotlib, and the apeglm/ashr/normal shrinkage decision. Use when visualizing differential-expression results (RNA-seq, ChIP-seq, ATAC-seq, proteomics) or any per-feature effect-size + p-value table.

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Build genome-browser-style multi-track figures with pyGenomeTracks (config-driven), Gviz (R), and IGV batch screenshotting. Covers BigWig coverage tracks, BED/peak overlays, gene-model rendering, Hi-C matrix tracks, BedPE link arcs, spike-in-aware normalization, and the bamCoverage --normalizeUsing trap. Use when producing publication figures of genomic loci with stacked aligned tracks (coverage, peaks, genes, interactions) for ChIP-seq, ATAC-seq, RNA-seq, Hi-C, or generic locus visualization.

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Analyzes time-series and longitudinal RNA-seq for differential expression and trajectory structure. Covers DESeq2 LRT with reduced models, time as factor vs continuous vs natural splines, maSigPro (Nueda 2014 for RNA-seq), ImpulseDE2 with explicit impulse-model failure modes, DREAM for repeated measures via linear mixed models, pseudoreplication avoidance, conditional vs marginal modeling, and trajectory clustering with DPGP, Mfuzz (with Schwämmle 2010 fuzzifier estimation), and splines+k-means. Use when modeling time-course or longitudinal expression, choosing factor vs spline, handling repeated measures from the same subject, avoiding pseudoreplication, clustering temporal trajectories, or selecting between dedicated time-course tools and pairwise+LRT.

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Read, write, and index compressed sequence files (gzip, bzip2, xz, BGZF) with Biopython and bgzip/samtools. Use when working with .gz, .bz2, or .bgz sequence files, when random access into a compressed FASTA/FASTQ is needed, or when SeqIO.index/faidx/tabix rejects a plain .gz. Covers the BGZF-vs-gzip seekability asymmetry, the 'rt'-not-'rb' handle trap, virtual offsets, and gzip-to-BGZF conversion.

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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.

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Detect single-nucleotide crosslink (CL) sites in CLIP-seq data using truncation patterns (iCLIP/eCLIP CITS), crosslink-induced mutations (HITS-CLIP CIMS deletions, PAR-CLIP T-to-C), or HMM/kernel-density methods (PureCLIP, PARalyzer, CTK). Use when single-nucleotide resolution is required for motif registration (mCross), allele-specific binding (BEAPR), variant-effect prediction, or comparing crosslink chemistry across CLIP variants.

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Map N6-methyladenosine (m6A) RNA modifications at single-nucleotide resolution using miCLIP (Linder 2015), miCLIP2 + m6Aboost machine learning (Kortel 2021), GLORI (Liu 2023, antibody-free chemical conversion), DART-seq (Meyer 2019, APOBEC1-YTH fusion), m6Anet (nanopore direct RNA), or MeRIP-seq with calibration. Use when distinguishing antibody-based from antibody-free m6A detection methods, applying the DRACH motif constraint, reconciling cross-method disagreements (DART 44% in DRACH vs GLORI), or detecting m6Am at the cap.

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Generate consensus FASTA sequences by applying VCF variants onto a reference with bcftools consensus, or build viral/amplicon consensus with iVar. Use when reconstructing a sample-specific reference or haplotype, deciding -H haplotype vs IUPAC vs all-ALT projection, masking no-coverage sites so a consensus does not manufacture false reference calls, or setting iVar min-depth/min-frequency policy for surveillance genomes.

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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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