「file」の検索結果

Configures 1Password CLI with direnv for fast, secure credential loading. Activates for: 1Password + direnv setup, slow secrets (>2 sec), .env.op files, op:// references, AWS credentials via env vars, --reveal flag issues, repeated biometric prompts, creating 1Password items programmatically, op item get errors. Not for: 1Password GUI usage, SSH keys (use 1Password SSH agent).

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。

Use when you need to review, improve, or build Spring Boot 4.0.x applications — including proper usage of @SpringBootApplication, component annotations (@Controller, @Service, @Repository), bean definition and scoping, configuration classes and @ConfigurationProperties (with @Validated), component scanning, conditional configuration and profiles, constructor injection, @Primary and @Qualifier for multiple beans of the same type, bean minimization, graceful shutdown, virtual threads, Jakarta EE namespace consistency, and scheduled tasks. This should trigger for requests such as Review Java code for Spring Boot application; Apply best practices for Spring Boot application in Java code. Part of cursor-rules-java project

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。

SSL/БСП subsystems guidance and search via 1c-mcp_ssl_server MCP. Use when working with standard library subsystems - users, files, print forms, background jobs, email, common utilities.

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。

Create or update a pull request for the current branch. Trigger when the user asks to create/open/make a PR, or to edit/update/rewrite/fix the PR description, body, or summary — for both new PRs (`gh pr create`) and existing ones (`gh pr edit --body-file`). Use for any verb that lands on a PR's text content: "open a PR", "make a PR", "update the PR description", "rewrite the PR body", "fix the description".

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。

Refactor a whole documentation page in this repository without losing source-verified behavior facts. Use for page rewrites, splits, reorganizations, or substantial shortening of README sections, docs pages, or instruction files. Do not use for ordinary documentation authoring, targeted corrections, or documentation review; use technical-documentation instead.

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。

Write, review, or audit this repository's technical documentation, including README.md, CONTRIBUTING.md, root and scoped AGENTS.md files, docs pages, and documentation drift. Use for source-backed documentation authoring, behavior verification, and cross-surface consistency. Do not use for code review, deslop diff cleanup, or whole-page rewrites, splits, or reorganizations handled by docs-refactor.

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。

Turn character reference images into reusable, rigged voxel 3D assets for Blender and Three.js through an imagegen turnaround and user-approval workflow. Use when Codex needs to preserve a character's likeness across front, side, and back views; create or revise Minecraft-like cube-headed models; prevent missing rear hair or clothing; split features between block geometry and face/clothing textures; generate GLB and editable .blend files; add walk/smash-compatible rigid-part pivots; or diagnose why a voxel conversion is not recognizable.

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。

Manages shadcn components and projects — adding, searching, fixing, debugging, styling, and composing UI, including chat interfaces. Provides project context, component docs, and usage examples. Applies when working with shadcn/ui, component registries, presets, --preset codes, or any project with a components.json file. Also triggers for "shadcn init", "create an app with --preset", or "switch to --preset".

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。

Triage a GitHub issue that already has the cc-issue-created label and is assumed ready to start. Inspect the comment history first to decide whether human confirmation is needed (cc-need-human-check, highest priority — reserved for issue-level deadlock, or for confirmation items answer-issue-questions already investigated and explicitly marked unanswerable); otherwise close the issue as not needed, delegate unanswered confirmation items in the last comment or the description to answer-issue-questions (cc-answer-issue-questions), refresh a description stale relative to settled comment-history content (cc-update-issue), or move to execution (cc-exec-issue). Any UI-changing issue is routed to the design-first flow (cc-create-ui-design) before execution; the exceptions are an issue whose description already names the .pen design to implement against, and a minor UI change that introduces no new visual decision (no new screen/section, no layout change, no new reusable component, no visual expression outside existing design tokens/components). Design files are never edited in the implementation PR. Dependency checks are out of scope.

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。

Builds an interactive HTML dashboard visualizing the Agent Skills ecosystem by fetching live data from github.com/agentskills/agentskills. Use this skill whenever the user wants to explore, research, or visualize Skills architecture, the SKILL.md spec, ecosystem adoption, repo stats, or any Skills intelligence dashboard. Trigger when the user mentions "skills dashboard", "skills ecosystem", "skills architecture overview", "agentskills repo", or wants to analyze how different tools implement Agent Skills. Optimized for Perplexity Computer — Computer fetches all data live, no static files required.

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。

Routes memory and retrieval tasks between MemPalace and QMD. Use this skill whenever the user asks WHERE something is in the codebase (route to QMD), WHY something was built a certain way or what was decided (route to MemPalace), or needs BOTH code and historical context (combined). Trigger on phrases like: 'where is X', 'find X in the code', 'search the codebase for X', 'what did we decide about X', 'why does X work this way', 'show me X and why we built it', 'look up X', 'what's in the handoffs about X', 'pull the relevant files for X'. Use proactively whenever a question could benefit from codebase search OR project memory — don't wait for the user to explicitly ask for a search.

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。

Use when a user-driven CloakBrowser profile needs MV3 Chrome writes/events through the native messaging bridge.

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。

Turns Hi-C/Micro-C FASTQ into a deduplicated, filtered .pairs file with pairtools and decides whether the library worked. Covers the bwa mem -SP5M / bwa-mem2 / chromap --preset hic alignment idiom (mates mapped as independent single-end reads), pairtools parse vs parse2 and the walks-policy choice (5unique pairwise vs all for Pore-C/Micro-C concatemers), pair-type classification (keep UU and rescued UC), dedup (PCR vs optical/by-tile), select by pair_type/MAPQ/distance, restriction-fragment handling (restrict, Arima dual-enzyme, Micro-C/DNase fragment-free), and allele-specific phasing (pairtools phase to two coolers). The library-QC decision uses % long-range cis as the one-number quality metric, trans as the noise floor, orientation balance as fragment-map-free dangling-end/self-circle QC, and % duplicates as a complexity proxy. Use when processing Hi-C/Micro-C/Omni-C reads into pairs, judging library quality, handling multi-enzyme or restriction-agnostic protocols, or generating allele-specific contacts.

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。

Assembles haplotype-resolved diploid and telomere-to-telomere (T2T) genomes from PacBio HiFi reads with hifiasm (HiFi-only, Hi-C, or trio phasing) and verkko (HiFi + ultralong ONT for T2T), extracting contigs from GFA and routing phasing QC to k-mer/trio metrics. Covers why a primary assembly is a haplotype mosaic that exists in no cell, partial-vs-full phasing (the .bp. vs .dip. filename convention), the purge-default trap on inbred samples, the --hom-cov coverage-estimate alarm, and verkko-vs-hifiasm for T2T. Use when assembling a diploid eukaryote from HiFi, phasing haplotypes with parents (trio) or Hi-C, deciding whether to chase T2T, or diagnosing switch errors invisible to N50/BUSCO/QV.

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。

Segment single cells from multiplexed IMC/MIBI tissue images using Mesmer/DeepCell, Cellpose, or ilastik+CellProfiler, covering whole-cell vs nuclear segmentation, the summed-membrane-channel decision, nuclear-expansion bias, lateral spillover, resolution-floor parameters, and downstream-proxy evaluation. Use when delineating cells after preprocessing, choosing a segmentation model, building a cell mask for quantification, diagnosing impossible double-positive populations, or troubleshooting over/under-segmentation.

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。

Loads, converts, and manipulates Hi-C contact matrices in cooler format (.cool/.mcool/.scool) and Juicer .hic, using cooler (Python + CLI), hic2cool, and hictk. Covers the single-resolution mcool URI (file.mcool::/resolutions/<bp>), the load-bearing divisive-vs-multiplicative weight-naming rule (KR/VC/VC_SQRT auto-divisive vs cooler's multiplicative weight), what survives .hic<->.cool conversion (FRAG matrices and norm vectors do not), raw-vs-balanced coarsening, the .pairs upper-triangle/chromsize-order contract, and chrom-naming/bin-table provenance. Use when loading a cooler, converting .hic to .mcool, selecting a resolution, building a cooler from pairs or a matrix, coarsening/zoomifying, importing Juicer norm vectors, or debugging all-NaN balanced matrices and chr1-vs-1 empty fetches.

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。

Performs set operations on genomic intervals - intersect (-wa/-wb/-wo/-wao/-loj/-c/-v/-u), subtract (-A), merge (-d, -c/-o), complement, cluster, multiinter, unionbedg, map, and groupby - with bedtools (CLI) and pybedtools/pyranges/bioframe (Python). Covers the sorted-input contract and the -sorted chromosome-order footgun, reciprocal/fractional overlap (-f/-F/-r/-e) and the A-vs-B asymmetry, -split for spliced/BED12/BAM features, and jaccard/fisher as mechanics only. Use when finding overlapping or unique regions between BED/peak/feature files, building consensus peaksets, removing blacklisted regions, transferring annotation values onto intervals, or computing interval-set similarity; route overlap-significance testing to overlap-significance.

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。

Renders Hi-C contact matrices honestly and reproducibly with matplotlib, cooltools, HiCExplorer, pyGenomeTracks, FAN-C, CoolBox, and plotgardener. Covers the raw/ICE-balanced/observed-over-expected transform choice, LogNorm vs symmetric-diverging colormaps with vmax/percentile clipping, resolution-to-feature matching (compartments 100-500kb, TADs 10-40kb, loops 5-10kb), square vs rotated-triangle track-stacking, NaN/white-stripe handling, virtual 4C, APA/saddle/on-diagonal pileups, two-condition side-by-side and log2-ratio maps, and interactive (HiGlass) vs scripted-static publication figures. Use when plotting a contact matrix, choosing a normalization or color scale, building a multi-track Hi-C figure, making a virtual 4C profile, piling up loops/boundaries, or comparing two conditions.

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。

Profiles a genome from raw reads BEFORE assembly with a k-mer spectrum (KMC or Jellyfish histogram), then models it with GenomeScope2 to estimate genome size, heterozygosity, repeat content, and ploidy, and Smudgeplot to infer ploidy from heterozygous k-mer pairs (diploid AB vs triploid AAB vs tetraploid AABB). Covers choosing k via Merqury best_k.sh, the k-mer-coverage vs sequencing-coverage confusion, reading het/repeat/contamination/organelle peaks, why noisy ONT must not be used for counting, and how the estimate becomes the NG50 denominator, the Flye -g value, the hifiasm --hom-cov/purge setting, and the 1.5-2x-too-big haplotig sanity check. Use when starting any de novo assembly, deciding whether short reads can work, estimating genome size for an unknown organism, diagnosing ploidy, or sanity-checking an assembly's size against expectation.

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。

Reads, queries, and writes bigWig indexed binary signal tracks (coverage, fold-change, conservation, methylation-rate) with pyBigWig (Python) and the UCSC Kent tools (bedGraphToBigWig, bigWigToBedGraph, bigWigInfo, bigWigSummary, bigWigAverageOverBed) and deepTools (multiBigwigSummary, computeMatrix, bigwigCompare). Covers the central trap that a wide query returns a precomputed zoom-level summary (by default the mean, which annihilates narrow peaks) not per-base data, when exact=True/values() is mandatory, the NaN-not-zero gap-handling fork, choosing mean vs max vs sum vs coverage by biological question, and the sorted-bedGraph plus chrom.sizes build requirement. Use when extracting signal at regions, computing mean signal per gene/peak, building a browser track from bedGraph, comparing tracks, or building TSS/gene-body metaprofiles.

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。

Load and preprocess imaging mass cytometry (IMC) and MIBI data from raw MCD/TXT through hot-pixel removal, spillover compensation, and variance-stabilizing transformation, covering readimc/steinbock ingestion, NNLS spillover compensation (CATALYST), IMC-Denoise, and the IMC arcsinh-cofactor question. Use when starting analysis from raw MCD files, building per-channel TIFF stacks, compensating channel spillover, choosing an arcsinh cofactor, or preparing single-cell intensities for phenotyping.

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。

Reads, inspects, and writes Flow Cytometry Standard (FCS) files from conventional, spectral, and mass cytometry (CyTOF), and parses FlowJo/Cytobank/Diva workspaces. Covers FCS 2.0/3.0/3.1/3.2 internals ($PnE linear-vs-log, $DATATYPE, $SPILLOVER vs SPILL vs $COMP, $TIMESTEP), channel/parameter metadata, the silent linearize/truncate defaults, and R (flowCore, flowWorkspace, CytoML) plus Python (FlowKit, readfcs) readers. Use when loading flow or mass cytometry data, mapping detector channels to antibodies, extracting the event matrix, choosing a reader, or bridging FCS to the scanpy/AnnData ecosystem before preprocessing.

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。

Assesses genetic health of populations for conservation with Ne estimation across time horizons (LDNe NeEstimator V2 option-file API + SNeP physical-linkage correction; recent trajectory via GONE/GONE2; deep history via Stairway Plot 2 / dadi / fastsimcoal2 / PSMC), F-statistics, runs of homozygosity binned by length class to date inbreeding, genetic-load decomposition (Bertorelle 2022 realized vs masked), the modern 100/1000 Ne rule (Frankham 2014), Ne/Nc 2-6 orders of magnitude in marine fish (Hauser & Carvalho 2008), tree-sequence forward simulations (SLiM 4 + pyslim + tskit), and the Sukumaran-Knowles caveat against MSC methods for management-unit definition. Use when estimating Ne by time horizon, detecting inbreeding via F_ROH, decomposing genetic load, justifying conservation thresholds, distinguishing ESU/MU/DPS, configuring NeEstimator V2, or correcting LDNe physical linkage.

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。

Aligns and QCs methylated-RNA-immunoprecipitation (MeRIP / m6A-seq) IP and input libraries using STAR or HISAT2 splice-aware mapping, samtools sort/index, IP/input matched-pair tracking, antibody-lot metadata recording, replicate concordance via deepTools multiBamSummary + plotCorrelation, IP enrichment QC via plotFingerprint and per-transcript IP/input ratio distributions, library-complexity saturation curves via PreSeq c_curve / lc_extrap, and the explicit do-NOT-deduplicate convention for standard non-UMI MeRIP. Use when preparing paired IP and input BAM files for exomePeak2 / MeTPeak / MACS3 peak calling, evaluating MeRIP replicate concordance and IP enrichment, deciding whether to deduplicate (standard MeRIP typically NOT — see Tips), choosing genome-vs-transcriptome alignment for downstream peak vs m6Anet workflows, recording antibody clone and lot metadata for downstream cross-batch reconciliation, detecting failed IPs via saturation curves and IP/input distribution shape, or generating IP-over-Input bigWig tracks for downstream visualisation.

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。