Tag: ChIPseeker

Cell culture Cell lines (MDA-MB-231, 4T1 and RPE-1) were purchased from the American Type Culture Collection (ATCC). TP53-knockout MCF10A, TP53-knockout RPE-1 and Trex1 knockout 4T1 cells were gifts from the Maciejowski laboratory at the Memorial Sloan Kettering Cancer Center (MSKCC). OVCAR-3 cells were a gift from J. D. Gonzales. All…

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hi, I have a question or suggestion for you all. I have some peaks and I would to annotate them. My goal is to extend the annotation 10000 upstream from the start of the gene and 10000 downstream from the end of the gene body. So I don’t want to…

Home Bioconductor 3.17 Released April 26, 2023 Bioconductors: We are pleased to announce Bioconductor 3.17, consisting of 2230 software packages, 419 experiment data packages, 912 annotation packages, 27 workflows and 3 books. There are 79 new software packages, 7 new data experiment packages, no new annotation packages, 2 new workflows,…

This is the development version of GenomicRanges; for the stable release version, see GenomicRanges. The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing…

ChIPseeker Warning Message 1 I’m using ChIPseeker and I’m getting the following warning. The package still runs and an output file is generated but I’d like to know what this is telling me – ChIPseeker • 45 views • link updated 2 hours ago by ATpoint 70k • written 4…

In several manuals (example) on ChIP-seq analysis they pre-select, for instance +1000bp and -1000bp from the TSS as the “promoter-bound” regions: peakAnno_bcl11b <- ChIPseeker::annotatePeak(peak = ‘bcl11b_peaks.narrowPeak’, TxDb=txdb, tssRegion=c(-1000, 1000) ) which produces an object with a slot @anno in which each peak is assigned either “Promoter”, “5’ UTR”, “3’ UTR”,…

I want to plot the EnrichedHeatmap using the GenomicRanges of my CNA data. The normalizeToMatrix function returned mat1, which is filled with 0, resulting in Error: You should have at least two distinct break values. when I try to plot it. library(EnrichedHeatmap) library(GenomicRanges) library(data.table) library(ChIPseeker) library(tibble) library(AnnotationHub) library(IlluminaHumanMethylation450kanno.ilmn12.hg19) library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb…

Can ChiPseeker be as highly customizable as “computeMatrix”? for example if I want to plot the distribution of genes on the TAD boundary? 0 @8f91699d Last seen 21 hours ago Hong Kong It’s like “computeMatrix” in deeptools, computeMatrix scale-regions -R TAD.boundaries.bed -S gene.density.bw gives the distribution of the eigenvalues (in…

How to annotate a MACS2 peak output file that is in tabular format? 0 I am fairly new to ChIP-seq analysis. I am using data from someone else and they only have the MACS2 peak file in tabular format. I have annotated peaks previously using MACS2 .bed files using ChIPseeker,…

I am using ChIPseeker to annotate MACS2 peaks files from publicly available data. To begin, I’m trying to first annotate the peaks the way that the authors did in the publication. This is what they say they did – “Gene annotation of the regions bound by indicated proteins were performed…

I am using ChIPseeker to annotate MACS2 peaks files from publicly available data. To begin, I’m trying to first annotate the peaks the way that the authors did in the publication. This is what they say they did – “Gene annotation of the regions bound by indicated proteins were performed…

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?…

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,…

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…

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…