来表示一个文件是成对的数字。read1 <- "ATAC_Data/ATAC_FQs/SRR891269_1.fastq.gz" read2 <- ...
Conclusion Manually curated metadata and uniformly identified binding sites of publicly available CLIP-seq data sets will be a foundation for further integrative and comparative analyses. With maintained up-to-date data sets and improved functionality, CLIPdb (http://clipdb.ncrnalab.org webcite) will...
However, due to differences between different CLIP-seq assays, existing computational approaches to analyze the data can only be applied to a subset of assays. Here, we present a probabilistic model called omniCLIP that can detect regulatory elements in RNAs from data of all CLIP-seq assays. ...
A Model-Based Approach to Identify Binding Sites inCLIP-Seq DataTao Wang 1 , Beibei Chen 1,2 , MinSoo Kim 1,2 , Yang Xie 1,2 , Guanghua Xiao 1 *1Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, United...
Also, models built using CLIP-seq data show strong predictive power between independent CLIP-seq data sets, but are not strongly predictive for expression change. Similarly, models built from expression data are not strongly predictive for CLIP-seq data sets, supporting the finding that the ...
Peak calling tool for CLIP-seq data Installation PEAKachu is available via bioconda and can be installed using conda create -n peakachu peakachu python=3 Alternativaly, PEAKachu can be installed from source $ make readme_rst $ make package $ pip3 install --user dist/PEAKachu-0.2.0....
Discovering the Interactions between Circular RNAs and RNA-binding Proteins from CLIP-seq Data using circScan 来自 学术范 喜欢 0 阅读量: 248 作者:B Li,Xiao-Qin Zhang,Shu-Rong Liu,S Liu,Liang-Hu Qu 摘要: Although tens of thousands of circular RNAs (circRNAs) have been identified in ...
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Fig. 2. CLIP-seq data A) Treatment of CLIP-seq data for the identification of CELF1 binding sites. B) Table summarizing the number of reads obtained with the CLIP-seq and the mRNA-seq libraries. “Total” is the total number of reads, “Trimmed” and “Filtered” the number of reads...
Computational Methods for CLIP-seq Data Processing RNA-binding proteins (RBPs) are at the core of post-transcriptional regulation and thus of gene expression control at the RNA level. One of the principal c... PH Reyes-Herrera,E Ficarra - 《Bioinformatics & Biology Insights》 被引量: 32发表...