文献检索文档翻译深度研究
Suppr Zotero 插件Zotero 插件
邀请有礼套餐&价格历史记录

新学期,新优惠

限时优惠:9月1日-9月22日

30天高级会员仅需29元

1天体验卡首发特惠仅需5.99元

了解详情
不再提醒
插件&应用
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
高级版
套餐订阅购买积分包
AI 工具
文献检索文档翻译深度研究
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利:CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2025

熊:用于高通量单细胞分析的综合多组学工具包。

Ursa: A Comprehensive Multiomics Toolbox for High-Throughput Single-Cell Analysis.

机构信息

Institute of Environmental Medicine, Karolinska Institutet, Solna 171 65, Sweden.

Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna 171 65, Sweden.

出版信息

Mol Biol Evol. 2023 Dec 1;40(12). doi: 10.1093/molbev/msad267.


DOI:10.1093/molbev/msad267
PMID:38091963
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10752348/
Abstract

The burgeoning amount of single-cell data has been accompanied by revolutionary changes to computational methods to map, quantify, and analyze the outputs of these cutting-edge technologies. Many are still unable to reap the benefits of these advancements due to the lack of bioinformatics expertise. To address this issue, we present Ursa, an automated single-cell multiomics R package containing 6 automated single-cell omics and spatial transcriptomics workflows. Ursa allows scientists to carry out post-quantification single or multiomics analyses in genomics, transcriptomics, epigenetics, proteomics, and immunomics at the single-cell level. It serves as a 1-stop analytic solution by providing users with outcomes to quality control assessments, multidimensional analyses such as dimension reduction and clustering, and extended analyses such as pseudotime trajectory and gene-set enrichment analyses. Ursa aims bridge the gap between those with bioinformatics expertise and those without by providing an easy-to-use bioinformatics package for scientists in hoping to accelerate their research potential. Ursa is freely available at https://github.com/singlecellomics/ursa.

摘要

单细胞数据的大量涌现伴随着计算方法的革命性变化,这些方法用于绘制、量化和分析这些前沿技术的输出。由于缺乏生物信息学专业知识,许多人仍然无法从这些进展中受益。为了解决这个问题,我们提出了 Ursa,这是一个自动化的单细胞多组学 R 包,包含 6 个自动化的单细胞组学和空间转录组学工作流程。Ursa 允许科学家在基因组学、转录组学、表观基因组学、蛋白质组学和免疫组学领域在单细胞水平上进行定量后的单细胞或多组学分析。它通过为用户提供质量控制评估、多维分析(如降维和聚类)以及扩展分析(如伪时间轨迹和基因集富集分析)的结果,为用户提供了一站式分析解决方案。Ursa 的目标是通过为有生物信息学专业知识的人和没有生物信息学专业知识的人提供一个易于使用的生物信息学包,来弥合这一差距,希望能加速他们的研究潜力。Ursa 可在 https://github.com/singlecellomics/ursa 上免费获取。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2c8e/10752348/1a862c3a0fa8/msad267f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2c8e/10752348/d128311510a1/msad267f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2c8e/10752348/1a514f287861/msad267f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2c8e/10752348/33fecdd32e5c/msad267f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2c8e/10752348/156c824e17f1/msad267f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2c8e/10752348/ea7fba7c516e/msad267f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2c8e/10752348/1a862c3a0fa8/msad267f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2c8e/10752348/d128311510a1/msad267f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2c8e/10752348/1a514f287861/msad267f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2c8e/10752348/33fecdd32e5c/msad267f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2c8e/10752348/156c824e17f1/msad267f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2c8e/10752348/ea7fba7c516e/msad267f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2c8e/10752348/1a862c3a0fa8/msad267f6.jpg

相似文献

[1]
Ursa: A Comprehensive Multiomics Toolbox for High-Throughput Single-Cell Analysis.

Mol Biol Evol. 2023-12-1

[2]
Beyond single cells: microfluidics empowering multiomics analysis.

Anal Bioanal Chem. 2024-4

[3]
Multiview learning for understanding functional multiomics.

PLoS Comput Biol. 2020-4-2

[4]
Single-cell multiomics: technologies and data analysis methods.

Exp Mol Med. 2020-9

[5]
Smccnet 2.0: a comprehensive tool for multi-omics network inference with shiny visualization.

BMC Bioinformatics. 2024-8-24

[6]
Phenonaut: multiomics data integration for phenotypic space exploration.

Bioinformatics. 2023-4-3

[7]
scMNMF: a novel method for single-cell multi-omics clustering based on matrix factorization.

Brief Bioinform. 2024-3-27

[8]
Single-cell multi-omics sequencing and its application in tumor heterogeneity.

Brief Funct Genomics. 2023-7-17

[9]
ezSingleCell: an integrated one-stop single-cell and spatial omics analysis platform for bench scientists.

Nat Commun. 2024-7-3

[10]
Vertical and horizontal integration of multi-omics data with miodin.

BMC Bioinformatics. 2019-12-10

引用本文的文献

[1]
Comprehensive analysis of multi-omics single-cell data using the single-cell analyst.

Imeta. 2025-4-28

[2]
Single Cell Atlas: a single-cell multi-omics human cell encyclopedia.

Genome Biol. 2024-4-19

本文引用的文献

[1]
ezSingleCell: an integrated one-stop single-cell and spatial omics analysis platform for bench scientists.

Nat Commun. 2024-7-3

[2]
Interactive analysis of single-cell data using flexible workflows with SCTK2.

Patterns (N Y). 2023-8-3

[3]
SingleCAnalyzer: Interactive Analysis of Single Cell RNA-Seq Data on the Cloud.

Front Bioinform. 2022-5-23

[4]
Computational solutions for spatial transcriptomics.

Comput Struct Biotechnol J. 2022-9-1

[5]
ICARUS, an interactive web server for single cell RNA-seq analysis.

Nucleic Acids Res. 2022-7-5

[6]
Interactive single-cell data analysis using Cellar.

Nat Commun. 2022-4-14

[7]
Single-cell immunology: Past, present, and future.

Immunity. 2022-3-8

[8]
Asc-Seurat: analytical single-cell Seurat-based web application.

BMC Bioinformatics. 2021-11-18

[9]
DISCO: a database of Deeply Integrated human Single-Cell Omics data.

Nucleic Acids Res. 2022-1-7

[10]
Single-cell chromatin state analysis with Signac.

Nat Methods. 2021-11

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

推荐工具

医学文档翻译智能文献检索