「upstream」の検索結果

ATM 版本升級與開源 release train 工作流。USE FOR: ATM frameworkVersion 升級、release impact 分類、SemVer 決策、CODEOWNERS / changeset / release gate 檢查、ATM upstream release docs 維護。

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。

Keep inherited changes narrow, correctly marked, traceable, and easy to rebase across repository layers.

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。

Decompose tasks into structured, outcome-defined process entries with complexity triage. Load when user says "decompose this", "break this down", "what steps do I need", "plan this out", "what's the process for", "how do I approach this", or when any complex task needs structured execution planning. Includes a problem-understanding pass before complexity triage. Routes to `problem-to-plan` when the user needs planning deliverables (spec + plan + TODO). Does NOT replace brainstorming — brainstorming is design approval (upstream), this is execution planning (downstream).

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。

Parses, queries, converts, and extracts from GTF and GFF3 gene-model annotation files - walking the gene/transcript/exon/CDS hierarchy with gffutils (queryable SQLite DB), converting formats and extracting transcript/CDS/protein FASTA with gffread, slurping to dataframes with gtfparse/pyranges, and sanitizing malformed files with AGAT. Covers the 1-based-inclusive vs 0-based BED coordinate conversion (start-1 only), deriving implicit features (introns/UTRs/TSS), phase-not-frame, the stop-codon-in-or-out-of-CDS convention, and the chr1-vs-1 seqid and gene-ID-version mismatches that silently produce all-zero count matrices and dropped joins. Use when extracting features or sequences from an annotation, converting GTF<->GFF3 or GTF->BED, traversing the gene tree, or diagnosing a coordinate/provenance mismatch upstream of counting or DE.

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Detects m6A modifications from Oxford Nanopore direct-RNA-sequencing (ONT DRS) signal data using m6Anet (Hendra 2022 *Nat Methods* 19:1590; multiple-instance-learning neural network over DRACH 5-mer signal). Covers the required upstream pipeline (Dorado / Guppy basecalling -> minimap2 transcriptome alignment with `-ax map-ont -uf -k14 --secondary=no` -> nanopolish eventalign with `--scale-events --signal-index` (m6Anet-required) plus `--summary` / `--threads` housekeeping -> m6anet dataprep -> m6anet inference), per-site vs per-read probability interpretation including the `mod_ratio` per-site stoichiometry column, the DRACH-only modeling constraint, minimum-coverage thresholds (20-50 reads per site for stable probability estimates), multi-condition comparison via xPore (Pratanwanich 2021 *Nat Biotechnol* 39:1394), Nanocompore (Leger 2021 *Nat Commun* 12:7198), ELIGOS (Jenjaroenpun 2021 *NAR* 49:e7), and Dorado native modification calling (RNA004 chemistry, 2024+), reference-transcriptome version pinning, the cDNA-vs-DRS chemistry distinction (cDNA-Nanopore CANNOT be used for modification detection), and orthogonal validation against MeRIP / GLORI. Use when calling m6A from ONT DRS without immunoprecipitation, choosing m6Anet vs xPore vs Nanocompore vs ELIGOS vs Dorado native, interpreting per-site `probability_modified` vs `mod_ratio` vs per-read modification probabilities, comparing methylation between conditions from ONT data, deciding between m6Anet for known DRACH sites and Dorado/Remora for genome-wide screening, pinning RNA002 vs RNA004 chemistry and basecaller model versions, or troubleshooting eventalign / dataprep failures.

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。

Pull pre-computed ortholog calls from public databases (OrthoDB, Ensembl Compara, OMA browser, eggNOG, PANTHER, KEGG Orthology, HomoloGene) via their REST APIs. Use when orthologs are already curated upstream, when the question is "what is the X ortholog of Y" rather than "how to infer orthology de novo", when batch-mapping gene IDs across species, or when comparing the resources for consensus calls. Encodes confidence-level semantics, 1:1 vs 1:many vs many:many, HomoloGene deprecation, and when to defect to de novo computation.

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Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL + bias-corrected testing), BaalChIP (Bayesian beta-binomial with copy-number-aware overdispersion), and AlleleSeq (personalized diploid genome). Handles imprinted-locus awareness, X-inactivation artifacts, cancer copy-number imbalance, and integration with downstream caQTL / bQTL mapping. Use when identifying variants with allelic effects on TF binding, fine-mapping causal regulatory variants, validating deep-learning variant predictions, or characterizing cis-acting regulatory effects.

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Creates sashimi-style plots showing RNA-seq read coverage and splice junction counts using ggsashimi (general-purpose, condition-grouped overlays), rmats2sashimiplot (rMATS-output-aware), MAJIQ-VOILA (LSV posteriors interactive HTML), leafviz (leafcutter clusters Shiny), Jutils (tool-agnostic heatmaps and sashimi for rMATS/leafcutter/SUPPA2/MAJIQ output), or pyGenomeTracks (multi-track publication figures). Tool choice depends on the upstream differential-splicing tool's output format and the publication vs interactive use case. Use when visualizing specific splicing events, validating differential splicing calls, or producing publication-quality figures.

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。

Integrate Convex static self hosting into existing apps using the latest upstream instructions from get-convex/self-hosting every time. Use when setting up upload APIs, HTTP routes, deployment scripts, migration from external hosting, or troubleshooting static deploy issues across React, Vite, Next.js, and other frontends.

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。

Identify all files a specific author contributed to on a branch vs its upstream, tracing code through renames. Use when asked who edited what, what code an author contributed, or to audit authorship before a merge. This skill should be run as a subagent — it performs many git operations and returns a concise table.

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[BETA] AEM Cloud Service expert skill — add explicit connect/read/socket timeouts to outbound HTTP clients constructed without one (Apache HttpClient 4.x/5.x, OkHttp, JDK java.net.http.HttpClient), including the JDK per-request read timeout on HttpRequest. Use for "add HTTP timeouts", "this external/outbound call has no timeout", or a scan that flags a timeout-less client. Highest-frequency CSO outage cause: a client on default (effectively infinite) timeouts holds request threads on a slow upstream until the Jetty pool saturates and the site goes down. The analyzer locates timeout-less construction sites; mechanical per-library remediation applies CSO-backed default timeouts (recipe.md). This skill is in beta. Verify all outputs before applying them to production projects.

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。

Hunt Host Header Injection — password reset poisoning → ATO, web cache poisoning via unkeyed Host/X-Forwarded-Host, routing-based SSRF (Host picks upstream → cloud metadata/internal services), path-override SSRF/ACL-bypass (X-Original-URL/X-Rewrite-URL), OAuth redirect_uri/issuer poisoning, and absolute-URL link poisoning in emails. High to Critical when it reaches ATO or mass cache poisoning. Built on public Host-header research (PortSwigger 'Practical web cache poisoning' + James Kettle, and the classic password-reset-poisoning class). Use on any forgot-password flow, CDN/reverse-proxy-fronted app, OAuth/OIDC endpoint, or absolute-URL-in-email feature.

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Comprehensive offensive methodology for software supply chain attacks covering the full kill chain from reconnaissance through exploitation. Addresses dependency confusion across npm, PyPI, and NuGet ecosystems where internal registry override allows an attacker to inject malicious packages that shadow private dependencies. Covers typosquatting techniques for popular packages, compromised package injection via maintainer account takeover or social engineering, and build system attacks through Makefile injection, setup.py install hooks, and npm postinstall scripts. Extends into CI/CD artifact tampering where build outputs are replaced or modified in transit, code signing abuse through stolen or self-signed certificates, upstream repository compromise via commit injection or force-push to trusted repos, and container image supply chain attacks including base image trojaning and registry confusion. Maps to MITRE ATT&CK T1195.001 (Supply Chain Compromise: Compromise Software Dependencies and Development Tools...

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。

Fetch, preview, merge, and test GitHub PRs locally. Great for trying upstream PRs before they're merged.

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。

Efficiently bring upstream NanoClaw updates into a customized install, with preview, selective cherry-pick, and low token usage.

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。

Check for and apply updates to installed skill branches from upstream.

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。