也可以用scPipe 软件的pipeline+Rsubread比对 对于CEL-seq or CEL-seq2 data,用scruff的pipeline 对于全长数据,用传统的bulk流程就可以了 载入R 可以用常规的read.table 也可以用DropletUtils(for 10X data) 后面几部是sc-seq的重头戏 5.3 质控 为什么要做质控? 因为不同原因(例如细胞损伤,PCR扩增效率等)造成...
这里作者没有介绍表达矩阵的上游处理(比对、定量等),不过如果使用R进行处理的话,一般推荐Rsubread这个包 (Liao, Smyth, and Shi 2013, 2014)。 不同的scRNA-seq方法有不同的技术手段: UMIs:具有相同UMI的reads比对到一个基因,这个转录本的表达量只计算一次。处理包含UMI的数据(例如10X数据)就需要从每个read或read...
想要更快更有效率,可以用alevin软件的pipeline 也可以用scPipe 软件的pipeline+Rsubread比对 对于CEL-seq or CEL-seq2 data, 用scruff的pipeline 对于全长数据,用传统的bulk流程就可以了 载入R 可以用常规的read.table 也可以用DropletUtils(for 10X data) 后面几部是sc-seq的重头戏 5.3 质控 为什么要做质控? 因...
A gapped index is recommended for use on a personal computer, which typically has 16GB of memory or less. subread-buildindex (buildindex function in Rsubread) only needs 5.7GB of memory to build a gapped index for human/mouse genome. subread-align (align in Rsubread) needs 8.2GB of memory...
1.1 能学到什么？能看这本书的都是对单细胞测序有所需求或这有这个意愿去学习相关知识的。这本书主要是整合目前常见的单细胞分析流程并尽可能详细的解释这些流程的每一个步骤，包括原理，所使用的工具以及给出1.2不能学到什么？当然是与单细胞测序分析无关的其他分析，毕竟一口不能吃成大胖子。因为这本书关于...
bioconductor包的大致介绍
Stickers for some Bioconductor packages - feel free to contribute and/or modify. - Bioconductor/BiocStickers
The entire pipeline mainly makes use of two R packages, Rsubread and limma, both available from the popular Bioconductor project.doi:10.1038/protex.2015.039Wei ShiProtocol ExchangeShi W. A Bioconductor R pipeline for analysis of RNA-seq data. 2015....
erential abundance analysis I Rsubread for read alignment, quanti?cation and mutation discovery I QuasR provides an integrated work ?ow using Rbowtie for alignment and GenomicRanges for read counts. I cummeRbund for post-processing of cu?inks isoform assemblies Epigenetics I 53 packages with ...
In addition, Rsubread is not supported for Windows. However, downstream analyses of the BAM files can be performed using any platform on which R can be installed. The entire workflow takes 7–8 hours to run and requires 10 GB of RAM. Author contributions A.T.T.L. developed and tested ...