Tag: ChIPseeker

ChIPseq annotation with replicates

ChIPseq annotation with replicates 0 Hi, What’s the best way to annotate chip peaks in case of replicates? I have 3 replicates each group. I understand Chipseeker is a very convenient tool, but I can’t find a clear example of how to merge replicates and annotate the peaks for visualization?…

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Genome-wide identification of enhancers and transcription factors regulating the myogenic differentiation of bovine satellite cells | BMC Genomics

1. Yin H, Price F, Rudnicki MA. Satellite cells and the muscle stem cell niche. Physiol Rev. 2013;93(1):23–67. CAS  PubMed  PubMed Central  Google Scholar  2. Hoppeler H, Fluck M. Plasticity of skeletal muscle mitochondria: structure and function. Med Sci Sport Exer. 2003;35(1):95–104. CAS  Google Scholar  3. Astruc T: Carcass Composition,…

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What is the codification in genestrand 1 and 2?

What is the codification in genestrand 1 and 2? 0 Hi there, I’m doing some peak annotation using ChIPseeker library(ChIPseeker) library(TxDb.Hsapiens.UCSC.hg38.knownGene) library(clusterProfiler) library(annotables) library(org.Hs.eg.db) txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene peaks= readPeakFile(“peaks_”, header = F) peakAnno <- annotatePeak(peaks, tssRegion=c(-3000, 3000), TxDb=txdb, annoDb=”org.Hs.eg.db”) peaks_annot <- as.data.frame(peakAnno) In my annotation file “geneStrand” is codified as…

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How to get output of annotated genes from ChIPseeker tool

How to get output of annotated genes from ChIPseeker tool 1 Hi, I am new at ChIP-Seq analysis. I used ChIPseeker package through R but I couldn’t figure out how to get output of annoteted genes. Please help me! Thank you. ChIPseeker peakannotation • 569 views • link updated 2…

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