For that purpose, we have developed PRADA (Pipeline for RNA-Sequencing Data Analysis), a flexible, modular and highly scalable software platform that provides many different types of information available by multifaceted analysis starting from raw paired-end RNA-seq data: gene expression levels, ...
If you use nf-core/rnafusion for your analysis, please cite it using the following doi:10.5281/zenodo.3946477 An extensive list of references for the tools used by the pipeline can be found in theCITATIONS.mdfile. You can cite thenf-corepublication as follows: ...
It is challenging to interpret and draw a meaningful conclusion without the proper understanding of various steps involved in the analysis of such data. This chapter deals with the pipeline to be followed to process the raw RNA sequencing (RNA-Seq) reads, align, assemble, and quantify them in...
FastQC:(Andrews 2010) used to generate quality summaries of data: Per base sequence quality report: useful for deciding if trimming necessary. Sequence duplication levels: evaluation of library complexity. Higher levels of sequence duplication may be expected for high coverage RNAseq data. Overrepresent...
scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data NTP脚本中用到的函数 1. Sys.time() 显示当前时区标准日期和时间 > Sys.time()[1]"2020-10-09 20:23:33 CST"#其中CST表示中国标准时间,是China Standard Time的缩写 ...
RNA-Seq Alignment 命令行参数 请注意,由于正在进行管道开发和改进,从GDC门户下载的文件中的版本号可能会有所不同。 Original Dr15plus # STAR-2.4.2a ### For users with access to the ICGC pipeline: python star_align.py \ --genomeDir<star_index_path>\ ...
PipeRNAseq A comprehensive pipeline for RNAseq data analysis. This pipeline has been used in the following publications: Li, J., Byrne, K.T., Yan, F., ...,Sun, Y.H., ..., 2018.Tumor cell-intrinsic factors underlie heterogeneity of immune cell infiltration and response to immunotherapy...
The pipeline supports the analysis for: 1) the distinction and identification of major cell types; 2) the identification of cell type specific gene signatures; and 3) the determination of driving forces of given cell types. We applied this pipeline to the RNA-seq analysis of single cells ...
bulk RNA-seq data from bipolar disorder affected individuals and neurotypical controls from the amygdala and the subgenual anterior cingulate cortex (sACC). For reproducibility, the vignette walks through how to download the example data and run SPEAQeasy before performing the follow-up analysis. ...
Although the costs of next generation sequencing technology have decreased over the past years, there is still a lack of simple-to-use applications, for a comprehensive analysis of RNA sequencing data. There is no one-stop shop for transcriptomic genomics. We have developed MAP-RSeq, a comprehe...