「datasets」の検索結果

A robust and outlier-aware method for testing differential tissue composition from single-cell data. This model can infer changes in tissue composition and heterogeneity, and can produce realistic data simulations based on any existing dataset. This model can also transfer knowledge from a large set of integrated datasets to increase accuracy further.

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Method for scalable identification of spatially variable genes (SVGs) in spatially-resolved transcriptomics data. The method is based on nearest-neighbor Gaussian processes and uses the BRISC algorithm for model fitting and parameter estimation. Allows identification and ranking of SVGs with flexible length scales across a tissue slide or within spatial domains defined by covariates. Scales linearly with the number of spatial locations and can be applied to datasets containing thousands or more

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Fit linear models to overdispersed count data. The package can estimate the overdispersion and fit repeated models for matrix input. It is designed to handle large input datasets as they typically occur in single cell RNA-seq experiments.

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Implements a variety of methods for combining p-values in differential analyses of genome-scale datasets. Functions can combine p-values across different tests in the same analysis (e.g., genomic windows in ChIP-seq, exons in RNA-seq) or fo

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performing all the steps of gene expression meta-analysis considering the possible existence of missing genes. It provides the necessary functions to be able to perform the different methods of gene expression meta-analysis. In addition, it contains functions to apply quality controls, download GEO datasets and show graphical representations of the results.

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Dino normalizes single-cell, mRNA sequencing data to correct for technical variation, particularly sequencing depth, prior to downstream analysis. The approach produces a matrix of corrected expression for which the dependency between sequencing depth and the full distribution of normalized expression; many existing methods aim to remove only the dependency between sequencing depth and the mean of the normalized expression. This is particuarly useful in the context of highly sparse datasets such

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HiContacts provides a collection of tools to analyse and visualize Hi-C datasets imported in R by HiCExperiment.

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Curated trending across GitHub repos and the Hugging Face Hub (models, datasets, spaces) - filtered, clustered, and labeled by momentum with a one-line why-notable per pick.

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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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Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core, Nextflow, FASTQ analysis, variant calling, gene expression, differential expression, GEO reanalysis, GSE/GSM/SRR accessions, or samplesheet creation.

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Write performant Eloquent queries with eager loading, reusable scopes, and strict lazy-loading prevention in Laravel. Use when defining model relationships, creating query scopes, or processing large datasets with chunk/cursor.

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Execute long-running tasks in background isolates to keep the UI responsive. Use when performing heavy computations, parsing large datasets, or choosing between async/await and isolates.

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Look up and read Hugging Face paper pages in markdown, and use the papers API for structured metadata such as authors, linked models/datasets/spaces, Github repo and project page. Use when the user shares a Hugging Face paper page URL, an arXiv URL or ID, or asks to summarize, explain, or analyze an AI research paper.

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Publish and manage research papers on Hugging Face Hub. Supports creating paper pages, linking papers to models/datasets, claiming authorship, and generating professional markdown-based research articles.

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Use this skill for Hugging Face Dataset Viewer API workflows that fetch subset/split metadata, paginate rows, search text, apply filters, download parquet URLs, and read size or statistics.

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Builds tables and data grids for displaying tabular information, from simple HTML tables to complex enterprise data grids. Use when creating tables, implementing sorting/filtering/pagination, handling large datasets (10-1M+ rows), building spreadsheet-like interfaces, or designing data-heavy components. Provides performance optimization strategies, accessibility patterns (WCAG/ARIA), responsive designs, and library recommendations (TanStack Table, AG Grid).

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Create standardized metadata for data assets. Use when documenting new datasets, building data catalogs, improving data discoverability, or creating data dictionaries for teams.

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End-to-end paper reproduction from arxiv URL through smoke runs to replication experiments. Handles missing or partial official code, missing training scripts, missing hyperparameters, and private datasets via similar-public-dataset substitution. Use when the user asks to reproduce, implement, replicate, or re-run a paper from scratch, or pastes an arxiv URL with reproduction intent.

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Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.

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Automated hypothesis generation and testing using large language models. Use this skill when generating scientific hypotheses from datasets, combining literature insights with empirical data, testing hypotheses against observational data, or conducting systematic hypothesis exploration for research discovery in domains like deception detection, AI content detection, mental health analysis, or other empirical research tasks.

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This skill should be used at the start of any computationally intensive scientific task to detect and report available system resources (CPU cores, GPUs, memory, disk space). It creates a JSON file with resource information and strategic recommendations that inform computational approach decisions such as whether to use parallel processing (joblib, multiprocessing), out-of-core computing (Dask, Zarr), GPU acceleration (PyTorch, JAX), or memory-efficient strategies. Use this skill before running analyses, training models, processing large datasets, or any task where resource constraints matter.

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Digital pathology image processing toolkit for whole slide images (WSI). Use this skill when working with histopathology slides, processing H&E or IHC stained tissue images, extracting tiles from gigapixel pathology images, detecting tissue regions, segmenting tissue masks, or preparing datasets for computational pathology deep learning pipelines. Applies to WSI formats (SVS, TIFF, NDPI), tile-based analysis, and histological image preprocessing workflows.

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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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Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis.

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