Tag: ChIPseeker

Bioconductor – clusterProfiler

DOI: 10.18129/B9.bioc.clusterProfiler     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see clusterProfiler. statistical analysis and visualization of functional profiles for genes and gene clusters Bioconductor version: 3.12 This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene…

Continue Reading Bioconductor – clusterProfiler

Chipseq peak calling and peak frequency region

I am working on Chip seq data, I have implemented the chipseq pipeline with spike in method and called peaks using MACS2. The same data has been analyzed before in my lab, and my peaks show a similar pattern as the previous ones . By this I meant that the…

Continue Reading Chipseq peak calling and peak frequency region

Transgenerational epigenetic effects imposed by neonicotinoid thiacloprid exposure

This study is aimed at revealing the transgenerational effects of thia. We chose the developmental window from embryonic days 6.5 to E15.5 because of its importance in germ cell program establishment. The mice breeding was described in the Materials and Methods section “Mouse treatment and dissection.” The design of the…

Continue Reading Transgenerational epigenetic effects imposed by neonicotinoid thiacloprid exposure

annotatePeak error for some problem

annotatePeak error for some problem 0 hello, everyone: when I use ChIPseeker to annotatePeak my chip-seq peaks, some error came. When I use this function, I encounter some issues and would like to seek advice. How can I resolve this problem? I would greatly appreciate your help. my code is…

Continue Reading annotatePeak error for some problem

frequency plot for peaks

Hello, I am computer science student and trying to work on BioMedical data and learning and applying the Bioinformatics techniques. I have ChipSEQ data generated by my lab , of histone modification , H3k27me3, with three different samples I have applied the whole pipeline and able to call peaks as…

Continue Reading frequency plot for peaks

Bioconductor – GenomicRanges

    This package is for version 2.14 of Bioconductor; for the stable, up-to-date release version, see GenomicRanges. Representation and manipulation of genomic intervals Bioconductor version: 2.14 The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyze high-throughput sequencing…

Continue Reading Bioconductor – GenomicRanges

Bioconductor – rtracklayer

DOI: 10.18129/B9.bioc.rtracklayer     R interface to genome annotation files and the UCSC genome browser Bioconductor version: Release (3.6) Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may…

Continue Reading Bioconductor – rtracklayer

Epigenetic regulation during cancer transitions across 11 tumour types

Specimen data All samples for MM, OV, BRCA, PDAC, UCEC, CRC, CESC/AD, SKCM and HNSCC, as well as 2 NATs for GBM and 1 NAT for ccRCC were collected with informed consent in concordance with Institutional Review Board (IRB) approval at the School of Medicine at Washington University in St…

Continue Reading Epigenetic regulation during cancer transitions across 11 tumour types

Error in Gviz (actually, rtracklayer)

Error in Gviz (actually, rtracklayer) | IdeogramTrack 0 @25075190 Last seen 7 minutes ago South Korea When I run this code (below) iTrack <- IdeogramTrack(genome = “hg19”, chromosome = “chr2”, name = “”) then I get the error Error: failed to load external entity “http://genome.ucsc.edu/FAQ/FAQreleases” Did someone else encounter this…

Continue Reading Error in Gviz (actually, rtracklayer)

NGS Training | Top NGS Courses | Online Training | RNASeq | Genome Variant Detection

        NGS Training Next Generation Sequencing (NGS), a recently evolved technology, have served a lot in the research and development sector of our society. NGS methods are highly parallelized enabling to sequence thousands to millions of molecules simultaneously. This technology results into huge amount of data, which…

Continue Reading NGS Training | Top NGS Courses | Online Training | RNASeq | Genome Variant Detection

Top 25 Bioconductor Interview Questions and Answers

Bioconductor is an open-source software project that provides tools for the analysis and comprehension of high-throughput genomic data. It’s a powerful tool, widely used in bioinformatics and computational biology to process and analyze intricate biological data. Bioconductor’s strength lies in its vast array of packages specifically tailored for genomics research,…

Continue Reading Top 25 Bioconductor Interview Questions and Answers

Assign gene to peak in bulk ATAC-seq

Assign gene to peak in bulk ATAC-seq 0 Hi all, I have some questions about bulk ATAC-seq that I don’t understand, hope that you can help. If we have a task to identify which genes in a sample (such as diseased) are in open chromatin region, is that using differential…

Continue Reading Assign gene to peak in bulk ATAC-seq

Methylation Analysis – Missing Chromosome and Position Information for some CpG sites

Hello Biostars community, I am currently working on a methylation analysis using data obtained from an Illumina EPIC array. The RNA samples underwent pre-processing and quality control by a company, and they provided us with two txt files containing the m-values and b-values, respectively. However, I encountered an issue when…

Continue Reading Methylation Analysis – Missing Chromosome and Position Information for some CpG sites

ChIP-seq data analysis

ChIP-seq data analysis 1 How to find peak-associated genes regulated in ChIP-seq data? Thanks! analysis ChIP-seq data • 42 views If you have a peak list, you can use chipseeker to annotate the peaks to genes. Login before adding your answer. Read more here: Source link

Continue Reading ChIP-seq data analysis

Chromatin reprogramming and bone regeneration in vitro and in vivo via the microtopography-induced constriction of cell nuclei

Dahl, K. N., Ribeiro, A. J. S. & Lammerding, J. Nuclear shape, mechanics, and mechanotransduction. Circ. Res. 102, 1307–1318 (2008). Article  CAS  PubMed  PubMed Central  Google Scholar  Alisafaei, F., Jokhun, D. S., Shivashankar, G. V. & Shenoy, V. B. Regulation of nuclear architecture, mechanics, and nucleocytoplasmic shuttling of epigenetic factors…

Continue Reading Chromatin reprogramming and bone regeneration in vitro and in vivo via the microtopography-induced constriction of cell nuclei

Epigenetic dysregulation from chromosomal transit in micronuclei

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…

Continue Reading Epigenetic dysregulation from chromosomal transit in micronuclei

Epigenetic regulation of human-specific gene expression in the prefrontal cortex | BMC Biology

Preuss TM. The human brain: rewired and running hot. Ann N Y Acad Sci. 2011;1225 Suppl 1(Suppl 1):E182-191. Article  PubMed  Google Scholar  Roth G, Dicke U. Evolution of the brain and intelligence in primates. Prog Brain Res. 2012;195:413–30. Article  PubMed  Google Scholar  Laland K, Seed A. Understanding human cognitive uniqueness….

Continue Reading Epigenetic regulation of human-specific gene expression in the prefrontal cortex | BMC Biology

best annotation approach for peaks

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…

Continue Reading best annotation approach for peaks

Bioconductor – Bioconductor 3.17 Released

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,…

Continue Reading Bioconductor – Bioconductor 3.17 Released

Bioconductor – GenomicRanges (development version)

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…

Continue Reading Bioconductor – GenomicRanges (development version)

ChIPseeker Warning Message

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…

Continue Reading ChIPseeker Warning Message

Why not use ONLY promoter-bound peaks when testing for enrichment in differentially-bound regions?

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”,…

Continue Reading Why not use ONLY promoter-bound peaks when testing for enrichment in differentially-bound regions?

Obtain the GenomicRanges from segmented CNA data and the corresponding TSS for EnrichedPlot

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…

Continue Reading Obtain the GenomicRanges from segmented CNA data and the corresponding TSS for EnrichedPlot

Can ChiPseeker be as highly customizable as “computeMatrix”? for example if I want to plot the distribution of genes on the TAD boundary?

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…

Continue Reading Can ChiPseeker be as highly customizable as “computeMatrix”? for example if I want to plot the distribution of genes on the TAD boundary?

How to annotate a MACS2 peak output file that is in tabular format?

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,…

Continue Reading How to annotate a MACS2 peak output file that is in tabular format?

Using ChIPseeker (max extension and curated regulatory domains included

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…

Continue Reading Using ChIPseeker (max extension and curated regulatory domains included

Question about ChIPseeker parameters

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…

Continue Reading Question about ChIPseeker parameters

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?…

Continue Reading ChIPseq annotation with replicates

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,…

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

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…

Continue Reading What is the codification in genestrand 1 and 2?

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…

Continue Reading How to get output of annotated genes from ChIPseeker tool