RNA-seq, QC and differential analysis pipeline. Contribute to sequana/rnaseq development by creating an account on GitHub.
On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to be...
自己在参考大牛的基础上,总结了RNAseq比对流程pipeline脚本。在做好前期准备工作后,可以一步完成从fastq到表达矩阵的所有步骤,目前仅支持human Bulk RNAseq数据,后续有机会会继续学习、完善,扩展更多选项。十分欢迎大家参考使用,并提供建议与意见。 https://github.com/lishensuo/fq2count 或者https://gitee.com/li-...
github链接:https://github.com/griffithlab/rnaseq_tutorial 由于可能国内进不去,我这里将关键代码保存下来。 目录截图 image.png 得到FPKM、TPM、Readscounts cd/workspace/rnaseq/ref-only-expression wget https://raw.githubusercontent.com/griffithlab/rnaseq_tutorial/master/scripts/stringtie_expression_matrix....
Bulk RNA-sequencing pipeline流程(含代码) 对于Bulk RNA-seq测序(用于比较转录组学,如不同物种的同种组织样本,也就是我们常说的常规转录组测序,注意和单细胞测序区分),我们常用的分析流程有很多,之前的文章也有介绍。偶然在github上发现一个总结的很完整的分析流程和大家分享。
网址: READemption - A RNA-Seq Analysis PipelineREADemption 是对 RNA-Seq 数据进行计算评估的管道,功能包括数据读取,对齐,覆盖率计算,基因表达定量、差异基因表达分析与可视化。 1.READemption下载安装sou…
RNA-seq数据分析全流程(代码篇) 前面一篇提到《RNA-seq数据分析全流程(思路篇)》,本文主要依据上面的思路做一个代码流程的分享,主要参考GDC的数据分析流程: 1)序列比对 # STAR-2.6.0c # 安装STAR:https://github.com/alexdobin/STAR # 文档:https://github.com/alexdobin/STAR/blob/master/doc/STARmanual....
这里可以使用作者包装好的pipeline的方式运行(推荐)。 代码语言:javascript 复制 #devtools::install_github('dviraran/xCell')library(xCell)fpkm2<-fpkm%>%column_to_rownames("gene")fpkm2[1:4,1:4]xCell=xCellAnalysis(fpkm2,rnaseq=TRUE,#RNA-seq ...
(http://mccarrolllab.com/wp-content/uploads/2016/03/Drop-seqAlignmentCookbookv1.2Jan2016.pdf), with modifications8and are provided as supplementary software:https://github.com/chensong611/Dropseq_pipeline. The step-by-step protocol is also available athttps://kpmp.org/resources/. Primers ...
作者用mixture control experiments的方法,来评估现存的主流的pipeline,选出了每个方面最好的工具,发在了NM上。 评估的工具类型: 3,913 combinations of data analysis methods normalization imputation clustering trajectory analysis data integration 评估的方法: ...