10X genomics公司不仅为单细胞转录组数据分析提供了配套的cell Ranger软件,同时也提供了专门的分析结果查看软件-Loupe Cell Browser,该软件是一个图形界面的软件,操作非常的方便,支持windows和mac两种操作系统,下载地址如下 https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest 安装好之...
10X genomics公司不仅为单细胞转录组数据分析提供了配套的cell Ranger软件,同时也提供了专门的分析结果查看软件-Loupe Cell Browser,该软件是一个图形界面的软件,操作非常的方便,支持windows和mac两种操作系统,下载地址如下 https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest...
Access Cell Ranger from your web browser with Cloud Analysis. See if Cloud Analysis is right for you Loupe Browser 10 ways to dig into your data with Loupe Browser Loupe Browser is a desktop application for Windows and MacOS that allows you to interactively visualize data. ...
For PCA, Cell Ranger ATAC first normalizes the data to median cut site counts per barcode and log-transform it. The pipeline uses a fast, scalable and memory efficient implementation ofIRLBA(Augmented, Implicitly Restarted Lanczos Bidiagonalization Algorithm) that allows in-place centering and feature...
Loupe Cell Browser,该软件是一个图形界面的软件,操作非常的方便,支持windows和mac两种操作系统。 安装好之后,双击启动,界面如下 在cell ranger软件的输出结果中,有一个名为cloupe.cloupe的文件,该文件就是用于输入到Loupe Cell Browser软件中的。 通过左上角的File->Open File, 或者Browser for a Loupe Cell Bro...
Cell Ranger ATAC pipeline has two cut sites: the start position of the fragment, and the end position of the fragment. These are the locations where the ATAC enzyme attached to open chromatin. For each cut site, the Peak Viewer imputes an open region, where the chromatin is presumed to ...
”单细胞分析、染色质分析” 视频和PPT分享 Science: 小鼠肾脏单细胞转录组+突变分析揭示肾病潜在的细胞靶标10X单细胞测序分析软件:Cellranger,从拆库...分析、批次校正单细胞数据可视化 绘制和理解单细胞分析常见图形生信基础知识 Linux/Windows下Rstudio和Linux命令的使用Linux/Windows下转录组分析流程的搭建 ...
Single-cell data were aligned with cellranger (7.0.0) and handled with Seurat (5.0.3). Cells expressing few transcripts or genes were excluded before normalization. Doublets were identified and excluded with scDblFinder (1.14.0)83. Harmony (1.0.3) was subsequently used to integrate datasets84...
The filtered matrix, barcode, and features file from the “count” command of Cell Ranger (10x Genomics, version 6.0.0) were then read in the AnnData format using the SCANPY package for further analysis. K-means clustering was done on the cells to cluster them into 4 clusters using the Lo...
当然,测试结果可以直接发送给cellranger的开发 1.3 VCDJ 可视化 cellranger vdj管道将为单细胞V(D)J实验生成.vloupe文件。 .vloupe文件将在完成的cellranger vdj运行的outs文件夹中找到。 Loupe V(D)J Browser for Windows - 3.0.0 (November 19, 2018) Windows 7 (64-bit) or later 2GB RAM Download –...