「detect」の検索結果

3,810 件・関連度順

概要と使いどころ

scrna-meta-analysis

無料

Conduct rigorous cross-study meta-analysis of scRNA-seq data from ENCODE, integrating multiple single-cell transcriptomic datasets for a tissue/cell type. Use when the user wants to answer "what cell types exist in my tissue and what genes define them?" by combining scRNA-seq data across donors, labs, and platforms. Follows the Mawla et al. 2019 framework for assessing cross-study reproducibility, TIN-based quality filtering, and detection-limit-aware interpretation. Handles batch correction (Harmony/Seurat), dropout awareness, cross-contamination artifacts, and platform-specific biases. Use this skill for ANY scRNA-seq integration task, cross-dataset comparison, cell atlas construction, or reproducibility assessment involving ENCODE single-cell data.

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。

ammawla/encode-toolkit212026年9月27日更新

compare-biosamples

無料

Compare ENCODE experiments across different biosamples, tissues, or cell lines to identify tissue-specific regulatory patterns. Use when the user wants cross-tissue comparison, cell-type comparison, tissue-specific elements, differential chromatin, biosample matching, disease vs normal comparison, developmental time course, constitutive vs variable regulation, or multi-tissue data availability mapping. Handles batch effect detection, biosample hierarchy, and comparison design.

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。

ammawla/encode-toolkit212026年9月27日更新

single-cell-encode

無料

Find and work with ENCODE single-cell genomics data including scRNA-seq and scATAC-seq. Use when the user asks about single-cell experiments, cell type resolution, clustering from ENCODE data, deconvolution of bulk signals using single-cell references, or comparing single-cell vs bulk profiles. Covers platform differences (10X Chromium, Smart-seq2, Drop-seq), quality limitations of single-cell data, multimodal integration (RNA+ATAC), and cross-study reproducibility concerns. Also use for cell type annotation, gene detection limits, dropout artifacts, and single-cell data structure in ENCODE.

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。

ammawla/encode-toolkit212026年9月27日更新

integrative-analysis

無料

Plan and execute integrative analysis combining multiple ENCODE experiments for cross-dataset or multi-omic workflows. Use when the user wants to combine experiments, perform cross-dataset comparison, multi-omic integration, peak overlap analysis, differential binding, signal correlation, chromatin state segmentation, enhancer-gene linkage, or any analysis that requires merging or comparing data from two or more ENCODE experiments. Covers same-assay cross-sample, multi-omic same-sample, cross-organism, and perturbation integration designs. Guides compatibility checks, batch effect detection, normalization, integration strategy selection, and provenance documentation.

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。

ammawla/encode-toolkit212026年9月27日更新

refresh

無料

Detect drift in .arkhe/roadmap/ context files and regenerate them from the current codebase state. Scaffolds context directory if missing. Use when user runs /roadmap:refresh, mentions "refresh context", "update context", "init roadmap", "stale context", or "scaffold roadmap".

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。