要在基因-细胞 scRNA-seq 矩阵expr和附带数据框meta上使用默认参数运行 Augur（其中包含cell_type和label...
barcodes.tsv就是cell id，features.tsv就是gene id，matrix.mtx就是计数counts矩阵。这三个文件的详细...
tradeSeq a method and software package for trajectory-based differential expression analysis for sequencing data 通过generalized additive models 拟合基因表达的平滑函数; 对模型参数进行具有生物学意义的假设检验; 对于0膨胀的问题,该方法使用权重,简单理解就是剔除0值; 输入为:原始表达矩阵,拟时间注释,细胞在轨迹...
题目:bridging data and dynamics in single cells through machine learning 时间: 10月10日星期二 11:00 地点:校本部教二楼 309 reports 摘要 part/2 the rapid development of single-cell sequencing technologies provides unprecedented resolut...
介绍一篇文献:Identifying phenotype-associated subpopulations by integrating bulk and single-cell sequencing data,2021年发表于Nature Biotechnology,DOI号:10.1038/s41587-021-01091-3。算法已经写成了R软件包,放在GitHub上供使用:https://github.com/sunduanchen/Scissor。
单细胞测序技术(single cell sequencing)是指在单个细胞水平上,对基因组、转录组、表观组进行高通量测序分析的一项新技术,它能够弥补传统高通量测序的局限性,揭示单个细胞的基因结构和基因表达状态,反映细胞间的异质性。2013年,单细胞测序技术被《Science》将其列为年度最值得关注的六大领域榜首;2015年再次登上Science...
Transcriptomic profiles have been generated by microarrays and more recently, next generation sequencing (NGS) based RNA-sequencing. These techniques largely explored gene expression profiles using bulk-tissue-samples. However, understanding intra-tissue heterogeneity has become essential for various research ...
short tandem repeat loci from tested patients in microsatellite instability testing experiment. Basic statistics of single cell sequencing data are provided in Online-only Table1. The cluster information and TCR typing data are presented in Supplementary File1, which has also been uploaded to Figshare...
传统的构建基因共表达网络的方法都是基于所有细胞的相似性,忽略了细胞之间的异质性,此方法提出了一种可以为每一个细胞构建此细胞对应的基因共表达网络的方法,并构建gene在不同细胞网络中的度矩阵,此度矩阵衡量了基因的重要程度,对度矩阵进行常规的聚类和分析操作为单细胞数据的特征分析提供了新的思路。【详见摘要】 ...
2017年7月,奥地利研究人员在Nature Methods上发表“Pooled CRISPR screening with single-cell transcriptome readout (doi:10.1038/ nmeth.4227)”文章,创造性地将CRISPR-Cas9和单细胞RNA测序两种极有前景的基因组学领域结合在一起,发明了这种被称作CROP-seq的单细胞测序方法 (CRISPR droplet sequencing, CRISPR液滴测...