VIPER (Visualization Pipeline for RNA-seq analysis) is an analysis workflow that combines some of the most popular tools to take RNA-seq analysis from raw sequencing data, through alignment and quality control, into downstream differential expression and pathway analysis. VIPER has been created in ...
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...
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: ...
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...
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 compreh...
conduct differential expression for a pair of sample. miRNAkey [4] and miRDeep* [5] create a Java interface that allow users to run data locally by dragging and clicking but limit to one or a couple of samples at time. wapRNA [6] can conduct both RNA and miRNA-seq analysis for a ...
Extracellular RNAs (exRNAs) have attracted great attention due to their essential role in cell-to-cell communication as well as their potential as non-invasive disease biomarkers. However, at present, there is no consensus on the best method to profile e
Seq analysis methods. To fill this gap, we have developed Granatum, a fully interactive graphical scRNA-Seq analysis tool. Granatum takes its name from the Latin word for pomegranate, whose copious seeds resemble individual cells. This tool employs an easy-to-use web browser interface for a ...
Basepair has released a new pipeline for investigating changes in alternative splicing (AS) in RNA-seq. This pipeline uses LeafCutter, a state-of-the-art tool for detecting splicing changes.
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。 我们依照作者的思路来进行: ...