Tag: ChIPpeakAnno

Linear Models for Microarray Data Bioconductor version: 2.5 Data analysis, linear models and differential expression for microarray data. Author: Gordon Smyth with contributions from Matthew Ritchie, Jeremy Silver, James Wettenhall, Natalie Thorne, Mette Langaas, Egil Ferkingstad, Marcus Davy, Francois Pepin, Dongseok Choi, Di Wu, Alicia Oshlack, Carolyn de Graaf, Yifang…

DOI: 10.18129/B9.bioc.TxDb.Hsapiens.UCSC.hg38.knownGene     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see TxDb.Hsapiens.UCSC.hg38.knownGene. Annotation package for TxDb object(s) Bioconductor version: 3.9 Exposes an annotation databases generated from UCSC by exposing these as TxDb objects Author: Bioconductor Core Team, Bioconductor Package Maintainer <maintainer at…

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…

Padeken, J., Methot, S. P. & Gasser, S. M. Establishment of H3K9-methylated heterochromatin and its functions in tissue differentiation and maintenance. Nat. Rev. Mol. Cell Biol. 23, 623–640 (2022). Article  CAS  PubMed  PubMed Central  Google Scholar  Tchasovnikarova, I. A. et al. Epigenetic silencing by the HUSH complex mediates position-effect variegation…

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…

DOI: 10.18129/B9.bioc.regioneR   This is the development version of regioneR; for the stable release version, see regioneR. Association analysis of genomic regions based on permutation tests Bioconductor version: Development (3.19) regioneR offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other…

DOI: 10.18129/B9.bioc.DelayedArray     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see DelayedArray. A unified framework for working transparently with on-disk and in-memory array-like datasets Bioconductor version: 3.11 Wrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to…

ChIP-seq peaks annotation 0 Hi everyone, I have a set of ChIP-seq peaks that have been annotated to my reference genome. To annotate the peaks, I have assigned a peak to a gene if the distance between the peak’s start and gene’s start is the shortest. However, in some cases,…

Introduction Protein levels are regulated at several nodes. One mode of protein level regulation acts through enhancing or reducing gene transcription. Gene transcription can be stimulated by binding transcription factors to promoters or enhancers of target genes and by posttranslational modifications of transcription factors and histones. Such modifications can be…

Genes in open chromatin region 0 Hi Biostars friends, I have a questions about bulk ATAc seq that hope you can help. I use Diffbind to get the table below (differential accessibility regions) and then use ChipPeakAnno to annotate the peaks in the P column. Could I conclude that gene…

DOI: 10.18129/B9.bioc.vulcan     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see vulcan. VirtUaL ChIP-Seq data Analysis using Networks Bioconductor version: 3.15 Vulcan (VirtUaL ChIP-Seq Analysis through Networks) is a package that interrogates gene regulatory networks to infer cofactors significantly enriched in a…

How to get genes associated with open chromatin regions? 1 Hi all, I ran ATAC-seq pipeline such as nf-core and got output files such as bam, bigwig, broadpeak. Would you suggest a way to get genes associated with open chromatin regions? I used ChIPpeakAnno but for DiffBind. Thank you so…

DOI: 10.18129/B9.bioc.BSgenome.Hsapiens.UCSC.hg38     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see BSgenome.Hsapiens.UCSC.hg38. Full genome sequences for Homo sapiens (UCSC version hg38, based on GRCh38.p12) Bioconductor version: 3.13 Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, based on GRCh38.p12)…

DOI: 10.18129/B9.bioc.trackViewer   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see trackViewer. A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data Bioconductor version: 3.16 Visualize mapped reads along with annotation as…

Peaks annotation on bacterial genome 1 Hi all, I’m trying to annotate peaks identified in ChIP-seq experiments in M. tuberculosis using ChIPpeakAnno on R. I would like to distinguish between peaks that are located in promoter regions or in coding regions. Is it that possible? Is there any code I…

Help with Diffbind result 0 @3fdb6f97 Last seen 8 hours ago United States Hi all, I am trying to find which genes are different in chromatin accessibility so I used nf-core/ATAC pipeline then feed the bam files and broadpeak files output into Diffbind. I got around 100k peaks, 21k genes…

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…

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…

Infrastructure for Biostrings-based genome data packages Bioconductor version: 2.5 Infrastructure shared by all the Biostrings-based genome data packages Author: Herve Pages Maintainer: H. Pages <hpages at fhcrc.org> To install this package, start R and enter: source(“http://bioconductor.org/biocLite.R”) biocLite(“BSgenome”) To cite this package in a publication, start R and enter: citation(“BSgenome”) Documentation…

Infrastructure for manipulating intervals on sequences Bioconductor version: 2.6 The package provides efficient low-level and highly reusable S4 classes for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more generally, data that can be organized sequentially, as well as views on these sequences. Efficient list-like classes are also provided…