「transcript」の検索結果

The epistack package main objective is the visualizations of stacks of genomic tracks (such as, but not restricted to, ChIP-seq, ATAC-seq, DNA methyation or genomic conservation data) centered at genomic regions of interest. epistack needs three different inputs: 1) a genomic score objects, such as ChIP-seq coverage or DNA methylation values, provided as a `GRanges` (easily obtained from `bigwig` or `bam` files). 2) a list of feature of interest, such as peaks or transcription start sites, provi

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This package implements a metabolic network analysis pipeline to identify an active metabolic module based on high throughput data. The pipeline takes as input transcriptional and/or metabolic data and finds a metabolic subnetwork (module) most regulated between the two conditions of interest. The package further provides functions for module post-processing, annotation and visualization.

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Precise knowledge on the binding sites of an RNA-binding protein (RBP) is key to understand (post-) transcriptional regulatory processes. Here we present a workflow that describes how exact binding sites can be defined from iCLIP data. The package provides functions for binding site definition and result visualization. For details please see the vignette.

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TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It c

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A set of tools for making TxDb objects from genomic annotations from various sources (e.g. UCSC, Ensembl, and GFF files). These tools allow the user to download the genomic locations of transcripts, exons, and CDS, for a given assembly, and

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The Model-based Analysis of ChIP-Seq (MACS) is a widely used toolkit for identifying transcript factor binding sites. This package is an R wrapper of the lastest MACS3.

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Extract the genomic locations of genes, transcripts, exons, introns, and CDS, for the gene models stored in a TxDb object. A TxDb object is a small database that contains the gene models of a given organism/assembly. Bioconductor provides a

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Live-data research via the glim.sh MCP - web search, full page extraction, X/Twitter, Reddit, GitHub, Amazon, and YouTube transcripts - synthesized into a cited digest. Pay-per-call from the connected account balance; OAuth Connect via the dashboard MCP panel.

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Find web sources with query-relevant page excerpts and optional full-page content, and discover workflows, data APIs, and indexes. Use for web research or finding structured records, listings, transcripts, and datasets. Supports semantic tool discovery, domain matching, and progressive catalogue browsing.

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Deep learning for single-cell analysis using scvi-tools. This skill should be used when users need (1) data integration and batch correction with scVI/scANVI, (2) ATAC-seq analysis with PeakVI, (3) CITE-seq multi-modal analysis with totalVI, (4) multiome RNA+ATAC analysis with MultiVI, (5) spatial transcriptomics deconvolution with DestVI, (6) label transfer and reference mapping with scANVI/scArches, (7) RNA velocity with veloVI, or (8) any deep learning-based single-cell method. Triggers include mentions of scVI, scANVI, totalVI, PeakVI, MultiVI, DestVI, veloVI, sysVI, scArches, variational autoencoder, VAE, batch correction, data integration, multi-modal, CITE-seq, multiome, reference mapping, latent space.

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Analyzes meeting transcripts and recordings to uncover behavioral patterns, communication insights, and actionable feedback. Identifies when you avoid conflict, use filler words, dominate conversations, or miss opportunities to listen. Perfect for professionals seeking to improve their communication and leadership skills.

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Package an existing talking-head / interview / podcast video with timed, designed GRAPHIC OVERLAY cards — kinetic titles, lower-thirds, data callouts, quotes, side panels, picture-in-picture — synced to the transcript, on a 16:9 / 9:16 / 4:5 canvas of your choice; the clip plays untouched underneath. Trigger on "graphic overlays", "on-screen graphics", "package / dress up my video". Not plain subtitles (/embedded-captions). Unclear → /hyperframes.

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Add captions or subtitles to an existing single-subject talking-head video without editing the footage. Use for plain verbatim captions, cinematic captions embedded behind the subject, VFX captions, “炸/特效/酷炫字幕,” or a named identity from the 35-style catalog. Route by visual identity, not by backend engine. The quiet `anchor` rail is the default; embed every word only when the user explicitly wants a fully cinematic treatment. The workflow runs locally end to end, including transcription and subject matting; split multi-shot footage before applying it.

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Agent Media OS, the single skill for every media need in a HyperFrames project. Resolve BGM, SFX, image, icon, brand logo, voice, color grade, or LUT into a frozen local file or paste-ready block + ledger record (one verb, `resolve`); generate via TTS / music / image models when the catalog misses; produce voiceover, transcription, captions, and background removal through one shared audio engine; operate on media (cut / reframe / transform); and reuse assets across projects. Also use for vague feedback that real footage looks dark, flat, boring, should feel retro/camcorder/print/ASCII, needs privacy, or needs a media reveal.

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Speech-to-text transcription via OpenAI Whisper. Supports two modes — Local CLI (no API key, runs on-device) and Cloud API (fast, scalable, requires OPENAI_API_KEY). Use when the user needs to transcribe audio files, translate speech, or convert audio to text.

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Analyzes meeting transcripts and recordings to uncover behavioral patterns, communication insights, and actionable feedback. Identifies when you avoid conflict, use filler words, dominate conversations, or miss opportunities to listen. Perfect for professionals seeking to improve their communication and leadership skills.

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Aggregates transcript and frame data into an interactive web dashboard. Use for content, topic, or sentiment analysis.

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Batch Whisper transcription of video or audio (WAV, podcasts) with a re-runnable provenance record. Use to transcribe recordings.

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Recall why a past change was made, drawing on Codex session history when available and falling back to commit diff and surrounding code. Use when the user asks to "recall the rationale", "find the rationale", "look up the rationale", "why did I do X", "why did we do X", "why was this changed", or "find the transcript for this commit".

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Evaluate, fix, answer, and reply to GitHub pull request review comments and conversation comments. Handles both change requests (fix or skip) and reviewer questions (explain using the rationale recalled from past Claude Code transcripts). Use when the user asks to "resolve PR comments", "fix review comments", "address PR feedback", "handle review comments", "address review feedback", "respond to PR comments", "answer review questions", or "address code review".

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Analyzes meeting transcripts and recordings to uncover behavioral patterns, communication insights, and actionable feedback. Identifies when you avoid conflict, use filler words, dominate conversations, or miss opportunities to listen. Perfect for professionals seeking to improve their communication and leadership skills.

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Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.

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Process and generate multimedia content using Google Gemini API. Capabilities include analyze audio files (transcription with timestamps, summarization, speech understanding, music/sound analysis up to 9.5 hours), understand images (captioning, object detection, OCR, visual Q&A, segmentation), process videos (scene detection, Q&A, temporal analysis, YouTube URLs, up to 6 hours), extract from documents (PDF tables, forms, charts, diagrams, multi-page), generate images (text-to-image, editing, composition, refinement). Use when working with audio/video files, analyzing images or screenshots, processing PDF documents, extracting structured data from media, creating images from text prompts, or implementing multimodal AI features. Supports multiple models (Gemini 2.5/2.0) with context windows up to 2M tokens.

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Analyzes conversation transcripts to extract user corrections, patterns, and preferences, then proposes skill improvements. Use this skill when users provide corrections, express preferences about code style, or when patterns emerge from successful approaches. Can be triggered manually with /reflect or automatically at session end when enabled.

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