873 件 ・ 関連度順
概要と使いどころ
Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.
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Work with the user's meetings through the Vexa MCP tools — send a bot to a call, follow the transcript while it runs, and write meetings into their notes (Obsidian, Notion, plain markdown) with speakers and action items. Use whenever the user mentions a meeting, a call, a transcript, meeting notes, or asks what was said.
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Analyze and triage AssemblyAI REST, transcript, Streaming v3, webhook, and LLM Gateway failures without leaking customer content. Use when an integration errors or stalls. Trigger with "AssemblyAI error" or "failed transcript".
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Analyze and operate a production AssemblyAI pre-recorded pipeline with explicit models, Speech Understanding, callbacks, and retention controls. Use when running asynchronous transcription. Trigger with "AssemblyAI async transcription" or "pre-recorded pipeline".
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Fetch transcripts from YouTube videos for summarization and analysis.
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Extract subtitles and transcripts from Bilibili and YouTube videos. Use when the user wants to get subtitles from B站 (Bilibili) or YouTube, extract Chinese/Japanese video transcripts, watch member-only Bilibili content, or perform Q&A on video content. Supports dual-platform subtitle extraction with yt-dlp.
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Turn one long asset - a YouTube video, podcast, newsletter, blog post, transcript or client call - into a week of LinkedIn posts. Use when the user says "repurpose this", "turn this into posts", "I have a video/newsletter/ transcript", or pastes a long piece of content and wants it on LinkedIn.
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Extract subtitles/transcripts from YouTube videos. Triggers: "youtube transcript", "extract subtitles", "video captions", "视频字幕", "字幕提取", "YouTube转文字", "提取字幕".
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Analyze a product walkthrough, bug report video, Loom, or ScreenPal using Minutes transcription plus visual review. Use when the user wants a recorded demo or bug clip turned into a durable brief with transcript, key frames, issues, and next steps.
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Fetch existing YouTube transcripts/subtitles or archive spoken video content as text, and download YouTube videos/audio or HLS streams (m3u8) with yt-dlp and ffmpeg. Use for transcript/subtitle retrieval, text-first video archiving, video/audio downloads, protected streams with authentication headers, and download failures including nsig, 403 or browser-cookie issues.
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Reads, searches and exports local Claude Code and Kimi CLI history without resuming work: timelines, verbatim user input, keyword or fuzzy recall, file recovery from transcripts, and which session ran a given command in a known time window. Use when the user asks what was said, wants a session ID or original context, needs proof of what a session contained, or needs past-session runtime evidence about commands, tool calls and hook runs — query this index instead of raw-scanning transcript files. Not for Codex (use read-codex-history); with no platform or several named, start at local-conversation-history.
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Create a framing document from conversation transcripts. Use when the user has transcripts (VTT, call notes, etc.) and wants to produce a frame that captures the problem worth solving and why it was chosen over alternatives.
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Turn a shaped project kickoff transcript into a reference document for the builder. Use when the user has a transcript (VTT, etc.) from a kickoff call and wants to produce a document that captures what was shaped and agreed.
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Agent 1 of the video editing pipeline. Removes silences and dead air from a talking-head recording. Use when asked to cut silences, trim pauses, remove dead air / gaps, or tighten the pacing of a raw video, given a word-level transcript. Produces an edit list (EDL), a re-timed transcript for downstream agents, and optionally the cut video via ffmpeg. Does NOT cut mistakes, repeats, or false starts — that is the cut-mistakes agent.
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Turn a raw recording's transcript into an edit decision list - dead air, filler cues and retakes, with timecodes. Use for "edit this", "cut the dead space", "tighten this video", "I rambled", or any request to shorten footage from a transcript.
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Fetch YouTube transcripts via APIFY API. Works from cloud IPs (Hetzner, AWS, etc.) by bypassing YouTube's bot detection. Free tier includes $5/month credits (~714 videos). No credit card required.
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Discovers, classifies, filters, and quantifies full-length transcript isoforms from PacBio Iso-Seq/Kinnex (HiFi) and Oxford Nanopore (cDNA/direct-RNA) long reads, using the isoseq+pigeon pipeline, SQANTI3, and ONT tools (IsoQuant, FLAIR, Bambu, StringTie2). Covers why a novel isoform is an artifact until proven otherwise (RT template-switching, intra-priming, and 5' degradation manufacture junctions and truncations), the SQANTI3 structural categories and their trust order, the Kinnex skera-split step, orthogonal CAGE/poly-A/short-read-junction validation, and why long-read isoform quantification needs EM. Use when building a full-length isoform catalog, classifying/filtering long-read transcripts, running Iso-Seq or ONT cDNA/dRNA analysis, or judging novel-isoform reliability.
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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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Simulate transcription factor perturbation effects on cell state in silico with CellOracle and Dynamo, and predict transcriptional responses to genetic perturbations with GEARS, scGen, and CPA. Covers the direction-not-magnitude principle, local-linear validity, the GRN/velocity error it inherits, baseline discipline (mean and additive baselines), and the validation gap. Use when predicting TF knockout or overexpression effects, ranking driver TFs for fate transitions, or planning perturbation experiments. For GRN construction see multiomics-grn; for experimental Perturb-seq see single-cell/perturb-seq.
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Query the Ensembl REST API for gene/transcript/protein lookup, sequence retrieval, comparative genomics (Compara), variant effect prediction (VEP), regulatory features, and cross-species ortholog/paralog calls. Use when pulling Ensembl-native data (Ensembl Gene IDs, version-pinned releases, archive endpoints for reproducibility), gene/transcript/exon structure with stable IDs, or VEP for variant annotation. Encodes the 15 req/sec rate limit, archive (e110.rest.ensembl.org) for reproducibility, Ensembl divisions (vertebrates / plants / fungi / metazoa / bacteria), and the symbol-vs-ID stability problem.
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Annotate CLIP-seq peaks or crosslink sites to RNA features (5'UTR, CDS, 3'UTR, intron, splice junction, snoRNA, tRNA, ncRNA, repeat elements) with ChIPseeker, RCAS, RBP-Maps (Yeo splicing regulatory maps), and bedtools, applying feature-priority hierarchies, transcript-context resolution, and metagene aggregation. Use when characterizing where in transcripts an RBP binds, comparing peak distribution across regions, generating splicing-regulatory maps relative to alternative-splicing events, or distinguishing exonic vs intronic vs UTR binding.
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Analyzes alternative splicing from PacBio Iso-Seq (HiFi, Kinnex/MAS-Iso-seq) and Oxford Nanopore (direct cDNA, direct RNA, R10.4.1+) long-read RNA-seq with full-isoform resolution. Tools include FLAIR (correct/collapse/quantify/diffSplice for PacBio + ONT), IsoQuant (de-novo or annotation-guided isoform discovery 2024 SOTA), Bambu (annotation-aware Bayesian discovery + quantification with Novel Discovery Rate), SQANTI3 (isoform classification: FSM/ISM/NIC/NNC + artifact flags), rMATS-long (event calling on long-read isoforms), and minimap2 (-ax splice:hq for HiFi; -ax splice -k14 for ONT cDNA; add -uf only for direct RNA or stranded cDNA preps). Solves microexon detection, recursive splicing, complex multi-exon isoforms, and DTU without transcript-quantification uncertainty. Use when short-read AS limitations (anchor length, complex isoforms, microexons, recursive splicing, transcript ambiguity) demand full-isoform resolution.
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Requested GitHub PR/issue agent transcripts: redact, trim, preview, and insert safely.
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Walk a Claude Code session transcript turn-by-turn from Agent Monitor data, summarizing each user, assistant, and tool message in order so a long conversation can be reviewed quickly. Anchors the recap to the session header (model, cost, turn_count). Use when reviewing what was actually said and done in a conversation.
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。