例如,我们可以基于相关的“Technology”来查看与“Sequencing”相关的包,进一步细分为“RNASeq”相关的包。Workflow选项(Bioconductor - BiocViews)展示了可以用来说明某种分析工作流的Bioconductor包。例如:SingleCellWorkflow,演示如何使用Bioconductor包进行单细胞RNA-
2、一般最常用的是基因表达,基因表达其实包括芯片和RNAseq,其实Bioconductor最早就是用来分析芯片数据的,因为R擅长处理矩阵,而芯片数据恰好就是“矩阵”。 3、我们以Gene Expression中第一个workflow为例,这个是利用Deseq2包来分析RNAseq数据的例子,点开之后其实是一遍文献,这是这种workflow另一个显著的特点,它本身是...
RNA-Seq workflow: gene-level exploratory analysis and differential expression Changing genomic coordinate systems with rtracklayer::liftOver Mass spectrometry and proteomics data analysis 这些流程基本上涉及到了现在生物信息学的主流方向,所以基本上掌握了这些包,就是一个合格的生物信息学人才啦! 更重要的是它有...
This protocol presents a state-of-the-art computational and statistical RNA-seq differential expression analysis workflow largely based on the free open-source R language and Bioconductor software and, in particular, on two widely used tools, DESeq and edgeR. Hands-on time for typical small ...
标准化。scRNA-seq数据不同文库之间存在覆盖率的系统差异,例如测序深度差异。这通常是由于细胞之间cDNA捕获或PCR扩增效率不同而引起的,而这又是由于起始RNA量低导致的。标准化的目的是消除这些系统差异,以使它们不干扰聚类或差异表达分析时细胞之间表达谱的比较。
RNA-Seq workflow: gene-level exploratory analysis and differential expression Changing genomic coordinate systems with rtracklayer::liftOver Mass spectrometry and proteomics data analysis 这些流程基本上涉及到了现在生物信息学的主流方向,所以基本上掌握了这些包,就是一个合格的生物信息学人才啦!
1 Introduction to RNA-Seq theory and workflowStart Chapter In this chapter we explore what we can do with RNA-Seq data and why it is exciting. We learn about the different steps and considerations involved in an RNA-Seq workflow. View Details Introduction to RNA-Seq50 XP Core Concepts50 XP...
SYSargs S4 class contains a targets file (eg, sample input files) and a param file (specifying parameter for command line or R tools). Preconfigured workflows are included for RNASeq, DNA NGS, ChIP-Seq, and Ribo-Seq. Can use parallelization on multiple CPU/computer nodes to accelerate run...
RNA-Seq workflow: gene-level exploratory analysis and differential expression. F1000Research. 2015;4: 1070. https://doi.org/10.12688/f1000research.7035.1. 42. Hansen M, Gerds TA, Nielsen OH, Seidelin JB, Troelsen JT, Olsen J. PcaGoPromoter - An R package for biological and regulatory ...
SingleCellExperiment是一个能够完成常用的70种单细胞测序R包的数据交换的R包,因为它能存储一个sc-seq数据的所有数据在一个class里,可以放单个细胞数据,也可以放不同细胞间基因表达量数据,还可以放不同批次的细胞等等,一个数据就是一个assay。class中分门别类的放好,而且方便调用,一个函数就能去你想要得数据。举...