Results : Integrative analysis of iCLIP-seq and RNA-seq data allowed the prioritization of 22 RNAs whose splicing pattern is likely directly controlled by CELF1 protein in the lens. Of these, seven RNAs that encode proteins linked to cytoskeleton (e.g. ABLIM1, ANK2, CLTA, CTNNA2, SPTBN1...
SEQing: interactive web-based tool for visualization of iCLIP and RNA-seq data. - malewins/SEQing
SEQing supports RNA-seq data that can be displayed in a different window tab. This allows, e.g. crossreferencing the iCLIP data with genes differentially expressed in mutants of the RBP and thus obtain some insights into a potential functional relevance of the binding sites. Additionally, detail...
SEQing:在交互式python框架中基于Web的iCLIP和RNA-seq数据可视化。 RNA结合蛋白在特定位点与目标RNA相互作用。这些结合位点可通过单个核苷酸分辨率交联免疫沉淀(iCLIP)在全基因组范围内确定。随后,必须将结合位点可视化。到目前为止,还没有可视化工具可以轻松访问但也支持受限访问,因此可以在协作者之间共享数据。在这里,我...
htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets. This python package can be used to generate files necessary for data analysis using the companion R/Bioconductor package DEWSeq. URL: https://github.com/EMBL-Hentze-group/htseq-clip Documentation: https://htseq-clip.readthedo...
最近为了RNA-seq和iCLIP-seq的分析任务,靠朋友关系找了一个私有服务器,只能开个普通账号,系统是CentOS 8,一切都要苦逼的重新配置。 以下记录我配置环境的全过程 1. 打开服务器上的linux系统,登陆非根用户账号,默认进入"home/username/"目录下; 2. 安装miniconda: wget https://mirrors.tuna.tsinghua.edu.cn/an...
Revised iCLIP-seq Protocol for Profiling RNAprotein Interaction Sites at Individual Nucleotide Resolution in Living Cellsdoi:10.21769/BioProtoc.4688iCLIPeCLIPPosttranscriptional regulationRNA-binding proteinsUV crosslinkingSyed Nabeel-ShahJack F. Greenblatt...
Results: Here we present SEQing, a customizable interactive dashboard to visualize crosslink sites on target genes of RNA-binding proteins that have been obtained by iCLIP. Moreover, SEQing supports RNA-seq data that can be displayed in a different window tab. This allows, e.g. cross...