Results for “upstream”

Installs, diagnoses, repairs, and personalizes the official Tencent IMA skill (a wrapper around upstream ima-skill, not a replacement), including fan-out search across IMA knowledge bases with priority boosting. Use when the user mentions IMA / 腾讯 IMA / ima-skill, needs IMA API key setup, 知识库搜索 / 笔记搜索, imports URLs into a KB to extract content, or hits "Skipped loading skill(s) due to invalid SKILL.md" (ima-skill's missing-YAML-frontmatter bug).

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Ships pull requests to open-source projects you don't maintain — CONTRIBUTING compliance, PR-size/scope checks, minimal-diff implementation, AI-disclosure PR descriptions, and rebase or bot-review replies. Use for 提 PR / 上游 PR / 贡献代码, "open a PR", "fix this upstream", "rebase against main", "respond to the bot review". Not for reviewing PRs as maintainer (use github-review-pr) or general GitHub CRUD (use github-ops).

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Plan and implement OpenMeld PostgreSQL business persistence, schemas and migrations, transactions, Hyperdrive access, and data cutover. Use for the shared relational database transition or PostgreSQL work; not for unrelated D1 performance fixes or OpenConnector's upstream database.

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Check for and apply upstream COG framework updates (skills, docs, scripts) without touching personal content

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Use when implementing a new Spark expression in DataFusion Comet. Walks through cloning latest Spark master to study the canonical implementation, checking the upstream datafusion-spark crate before writing native code, building the Comet serde and Rust wire-up from the contributor guide, then running audit-comet-expression to drive a test-coverage iteration loop.

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Use when optimizing the performance of an existing native scalar expression in the datafusion-comet-spark-expr crate (native/spark-expr/) — casts, string/JSON/array/math kernels that run per-row or per-batch. Covers benchmarking, keeping output bit-identical, and the no-regression gate. Not for adding new expressions (use implement-comet-expression) or wiring upstream functions (use wire-datafusion-function).

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Use when wiring an existing DataFusion or datafusion-spark function into Comet for a Spark expression. Identifies the right wiring pattern (one-line passthrough, datafusion-spark UDF registration, or custom serde with input massaging / restrictions), applies the Scala serde, registers the UDF in jni_api when needed, and adds SQL file tests. Assumes the function already exists upstream — if not, switch to `implement-comet-expression`.

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End-to-end LinkedIn outreach campaign builder. Takes leads from Supabase, upstream skills, or CSV. Aligns on campaign goal and tone, writes personalized LinkedIn message sequences (connection request + follow-ups + optional InMail), presents for review, and exports for the user's outreach tool (Dripify, Botdog, Expandi, or manual CSV). Logs to Supabase outreach_log.

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Assemble a split-screen creator ad from a config — a two-zone vertical composite where a supplied AI-creator lip-sync take fills the BOTTOM ~48% while real 16:9 product/demo clips run uncropped in the TOP ~52%, each top clip contain-fit with a darkened blurred cover-scale fill of the same clip (never black bars), a 3px brand-color divider between the zones, the creator slice cover-fit per the per-scene VO timing, scenes hard-concatenated with the body audio being the concatenated creator VO slices, an end card held on the last sharp frame ~3s, then the ASSEMBLED cut transcribed with local Whisper (not the raw VO — concat drops inter-scene silence) and word-level captions burned in the chosen style. This is the FREE deterministic assembly + caption stage (two-zone composite + blurred fill + divider + hard-concat + end card + captions); the VO comes from create-vo-elevenlabs, the anchor from create-image-gpt-image-fal, and the whole-VO lip-sync from a paid VEED Fabric 1.0 take (a no-atom upstream input). Use for the split-screen-creator format.

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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-seq (DRS) signal using m6Anet (multiple-instance-learning over DRACH 5-mer signal). Covers the upstream pipeline (Dorado/Guppy basecalling -> minimap2 map-ont -> nanopolish eventalign -> m6anet dataprep -> m6anet inference), per-site vs per-read probability including the mod_ratio stoichiometry column, the DRACH-only constraint, minimum-coverage thresholds (20-50 reads/site), multi-condition comparison via xPore/Nanocompore/ELIGOS, Dorado native modification calling (RNA004, 2024+), and the cDNA-vs-DRS distinction (cDNA Nanopore CANNOT detect modifications). Use when calling m6A from ONT DRS without immunoprecipitation, choosing m6Anet vs xPore vs Nanocompore vs ELIGOS vs Dorado native, interpreting probability_modified vs mod_ratio vs per-read probabilities, deciding between m6Anet (known DRACH sites) and Dorado/Remora (genome-wide screening), pinning RNA002 vs RNA004 chemistry and basecaller versions, or troubleshooting eventalign/dataprep failures.

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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/MntJULiP/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.

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Build, migrate, and deploy Next.js apps on Cloudflare Workers with vinext. Use when starting a Next.js project on Cloudflare, moving an existing app to Workers, choosing between vinext and OpenNext, or setting up vinext for Workers. For setup, migration, or deployment, install vinext's upstream skills with `npx skills add cloudflare/vinext` if missing, then read and follow the applicable skill and docs.

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Push the current working tree directly to a GitHub PR whose head lives on a **fork**, without creating a new branch and without pushing to `origin` (which is usually the upstream). Invoke when the user says things like "push straight to PR

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Use when updating this codex-app Linux port from the latest upstream Codex Mac DMG, preserving local Linux patches, installing the refreshed desktop app, and publishing the tag-driven Linux release artifacts.

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Audits existing table permissions on a Power Pages site by analyzing them against site code and Dataverse metadata, then GRADES the configuration with deterministic 1–5 scores across 3 security/usability/correctness categories (9 dimensions). Detection is anchored by a recurring-issue catalog so findings and severities stay consistent run-to-run. Generates an HTML report with an at-a-glance verdict and per-category scores in the Overview plus a single list of **major/minor** issues (each major issue labelled permissions-only or upstream-caused with a short justification), and suggested fixes. Use when the user wants to review, verify, check, score, or grade table permissions for security issues.

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Build or change a customer-system integration with explicit data mapping, permissions, retries and reconciliation. Use for connectors, imports, write-back and upstream APIs.

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Install an improved variant of one named skill: resolve it by local path, repo, or name, run skill-creator's retrofit on a throwaway copy, then install the improved result. Don't use for improving in place, upstream PRs, or plain asm install.

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Authors or reviews Know/Understand/Do charts for competency-based learning targets across developmental bands. Handles seven input types from raw curriculum documents to existing LT sets. Routes to upstream skills when stronger inputs are available.

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When a solution seems impossible and the path forward is blocked. Refuses to take no for an answer: classifies what kind of "no" you hit, then runs lateral-thinking techniques (assumption autopsy, inversion, first principles, constraint toggling, analogical transfer, and more) until the wall cracks or is proven load-bearing. Generates at least 10 angles before evaluating any. AGENTS: use this on yourself when an API doesn't support what you need, an approach has failed twice, or a "that's not possible" sentence is forming — run the fast path BEFORE reporting a dead end. Archives walls to ~/.config/makerskills/unstuck/archive/. Sits upstream of decide. Triggers on "/unstuck," "I'm stuck," "this seems impossible," "we hit a wall," "there's no way to," "they said no," "dead end," "out of options," "I've tried everything," "work around this."

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When you want to set up an agent loop, cron-scheduled task, or recurring workflow that runs autonomously. Judgment layer on top of Claude Code's ScheduleWakeup, CronCreate, and /loop — or, on other hosts, cron/GitHub Actions plus a headless agent CLI. Picks dynamic pacing, fixed cron, or a one-shot loop; designs idempotent loop bodies; sets bail-out conditions so loops don't run forever. Examples — weekly review pulse, daily brief, hourly metric monitor, periodic vault compile, upstream-check for an adapted skill. Triggers on "/loopify," "set up a loop," "schedule this task," "run this daily," "run this weekly," "cron this," "make this recurring," "automate this on a schedule," "keep this running until X." Part of the -ify trifecta (skillify / toolify / loopify). NOT for authoring a new skill — that's skillify. NOT for adding a tool/integration — that's toolify.

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Use when the user wants a video of a website (site tour, portfolio, docs or landing-page showcase) captured from a URL. Deprecated upstream since v0.7.59: folded into /product-launch-video, which owns URL promo work.

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