# -------------------------------------------- # CITATION file created with {cffr} R package # See also: https://docs.ropensci.org/cffr/ # -------------------------------------------- cff-version: 1.2.0 message: 'To cite package "ChIPpeakAnno" in publications use:' type: software license: GPL-2.0-or-later title: 'ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data' version: 3.39.2 doi: 10.1186/1471-2105-11-237 abstract: The package encompasses a range of functions for identifying the closest gene, exon, miRNA, or custom features—such as highly conserved elements and user-supplied transcription factor binding sites. Additionally, users can retrieve sequences around the peaks and obtain enriched Gene Ontology (GO) or Pathway terms. In version 2.0.5 and beyond, new functionalities have been introduced. These include features for identifying peaks associated with bi-directional promoters along with summary statistics (peaksNearBDP), summarizing motif occurrences in peaks (summarizePatternInPeaks), and associating additional identifiers with annotated peaks or enrichedGO (addGeneIDs). The package integrates with various other packages such as biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest, and stat to enhance its analytical capabilities. authors: - family-names: Zhu given-names: Lihua Julie email: jianhong.ou@duke.edu - family-names: Ou given-names: Jianhong email: julie.zhu@umassmed.edu - family-names: Hu given-names: Kai email: kai.hu@umassmed.edu - family-names: Li given-names: Junhui email: junhui.li@umassmed.edu - family-names: Yu given-names: Jun - family-names: Liu given-names: Haibo - family-names: Pagès given-names: Hervé - family-names: Gazin given-names: Claude - family-names: Lawson given-names: Nathan - family-names: Thompson given-names: Ryan - family-names: Lin given-names: Simon - family-names: Lapointe given-names: David - family-names: Green given-names: Michael preferred-citation: type: article title: 'ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data' authors: - family-names: Zhu given-names: Lihua - family-names: Gazin given-names: Claude - family-names: Lawson given-names: Nathan - family-names: Pagès given-names: Hervé - family-names: Lin given-names: Simon - family-names: Lapointe given-names: David - family-names: Green given-names: Michael journal: BMC Bioinformatics volume: '11' year: '2010' issue: '1' url: http://www.biomedcentral.com/1471-2105/11/237 doi: 10.1186/1471-2105-11-237 issn: 1471-2105 abstract: BACKGROUND:Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) or ChIP followed by genome tiling array analysis (ChIP-chip) have become standard technologies for genome-wide identification of DNA-binding protein target sites. A number of algorithms have been developed in parallel that allow identification of binding sites from ChIP-seq or ChIP-chip datasets and subsequent visualization in the University of California Santa Cruz (UCSC) Genome Browser as custom annotation tracks. However, summarizing these tracks can be a daunting task, particularly if there are a large number of binding sites or the binding sites are distributed widely across the genome.RESULTS:We have developed ChIPpeakAnno as a Bioconductor package within the statistical programming environment R to facilitate batch annotation of enriched peaks identified from ChIP-seq, ChIP-chip, cap analysis of gene expression (CAGE) or any experiments resulting in a large number of enriched genomic regions. The binding sites annotated with ChIPpeakAnno can be viewed easily as a table, a pie chart or plotted in histogram form, i.e., the distribution of distances to the nearest genes for each set of peaks. In addition, we have implemented functionalities for determining the significance of overlap between replicates or binding sites among transcription factors within a complex, and for drawing Venn diagrams to visualize the extent of the overlap between replicates. Furthermore, the package includes functionalities to retrieve sequences flanking putative binding sites for PCR amplification, cloning, or motif discovery, and to identify Gene Ontology (GO) terms associated with adjacent genes.CONCLUSIONS:ChIPpeakAnno enables batch annotation of the binding sites identified from ChIP-seq, ChIP-chip, CAGE or any technology that results in a large number of enriched genomic regions within the statistical programming environment R. Allowing users to pass their own annotation data such as a different Chromatin immunoprecipitation (ChIP) preparation and a dataset from literature, or existing annotation packages, such as GenomicFeatures and BSgenome, provides flexibility. Tight integration to the biomaRt package enables up-to-date annotation retrieval from the BioMart database. start: '237' repository: https://bioc.r-universe.dev contact: - family-names: Zhu given-names: Lihua Julie email: jianhong.ou@duke.edu - family-names: Ou given-names: Jianhong email: julie.zhu@umassmed.edu - family-names: Hu given-names: Kai email: kai.hu@umassmed.edu - family-names: Li given-names: Junhui email: junhui.li@umassmed.edu references: - type: generic title: Integrative analysis of ChIP-chip and ChIP-seq dataset authors: - family-names: Zhu given-names: Lihua collection-title: Tilling Arrays collection-type: collection section: '4' editors: - family-names: Lee given-names: Tin-Lap - family-names: Luk given-names: Alfred Chun Shui publisher: name: Humana Press journal: Methods in Molecular Biology volume: '1067' year: '2013' url: http://link.springer.com/protocol/10.1007%2F978-1-62703-607-8_8 doi: 10.1007/978-1-62703-607-8_8 issn: 1064-3745 abstract: Epigenetic regulation and interactions between transcription factors and regulatory genomic regions play crucial roles in controlling transcriptional regulatory networks that drive development, environmental responses, and disease. Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) and ChIP followed by genomic tiling microarray hybridization (ChIP-chip) are the two of the most widely used technologies for genome-wide identification of DNA protein interactions and histone modification in vivo. Many algorithms and tools have been developed and evaluated that allow identification of transcription factor binding sites from ChIP-seq or ChIP-chip datasets. However, binding site identification is only the first step; the ultimate goal is to discover the regulatory network of the transcription factor (TF). Here, we present a common workflow for downstream analysis of ChIP-chip and ChIP-seq with an emphasis on annotating binding sites and integration with gene expression data to identify direct and indirect targets of the TF. These tools will help with the overall goal of unraveling transcriptional regulatory networks using datasets publicly available in GEO. start: '-19'