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Protocols

ChIPpeakAnno specifications

Information


Unique identifier OMICS_00804
Name ChIPpeakAnno
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 3.14.2
Stability Stable
Requirements
AnnotationDbi, limma, methods, stats, gplots, grid, Biobase, Rsamtools, testthat, GenomeInfoDb, rtracklayer, BiocStyle, GenomicAlignments, SummarizedExperiment, BSgenome, BSgenome.Hsapiens.UCSC.hg19, idr, biomaRt, GenomicFeatures, rmarkdown, knitr, S4Vectors(>=0.17.25), IRanges(>=2.13.12), multtest, matrixStats, BiocInstaller, GO.db, org.Hs.eg.db, DBI, graph, R(>=3.2), Biostrings(>=2.47.6), GenomicRanges(>=1.31.8), VennDiagram, BiocGenerics(>=0.1.0), RBGL, regioneR, ensembldb, seqinr, DelayedArray, reactome.db, BSgenome.Ecoli.NCBI.20080805, org.Ce.eg.db, BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, trackViewer, motifStack, OrganismDbi
Maintained Yes

Versioning


No version available

Documentation


Publication for ChIPpeakAnno

ChIPpeakAnno citations

 (102)
call_split

Different chromatin and DNA sequence characteristics define glucocorticoid receptor binding sites that are blocked or not blocked by coregulator Hic 5

2018
PLoS One
PMCID: 5940187
PMID: 29738565
DOI: 10.1371/journal.pone.0196965
call_split See protocol

[…] ong with the DESeq2 option during DiffBind analyses to identify the set of differentially bound peaks and create the MA plots. Venn diagrams overlapping the different sets of peaks were created using ChIPpeakAnno []. Both DiffBind and ChIPpeakAnno are packages available on Bioconductor [, ]. The Integrative Genomics Viewer was used to visualize the ChIP-seq data []. Motif analysis was performed us […]

call_split

The transcription factor Spores Absent A is a PKA dependent inducer of Dictyostelium sporulation

2018
Sci Rep
PMCID: 5923282
PMID: 29704004
DOI: 10.1038/s41598-018-24915-w
call_split See protocol

[…] to call peaks by MACS2 with a q-value cut off of <0.01, allowing a 200 bp shift in positions of peak summits between experiments. Peaks were annotated to the gene with the closest start codon, using ChIPpeakAnno. Gene ontology (GO) enrichment was determined using the Amigo tool at the GO consortium (www.geneontology.org/) with a threshold cutoff of p ≥ 0.05. […]

library_books

A B ARR mediated cytokinin transcriptional network directs hormone cross regulation and shoot development

2018
Nat Commun
PMCID: 5913131
PMID: 29686312
DOI: 10.1038/s41467-018-03921-6

[…] , 0.01, 0.001. The aligned reads with at least two biological replicates were processed using the irreproducibility discovery rate (IDR). The p-value cutoff was 1e-16. Peaks were then annotated using ChIPpeakAnno package. In order for us to classify a peak as associating with a gene, the peak summit must have been within 1.5 kb upstream and downstream of the gene’s annotation. The gene length was […]

call_split

KAP1 Regulates Regulatory T Cell Function and Proliferation in Both Foxp3 Dependent and Independent Manners

2018
Cell Rep
PMCID: 5947873
PMID: 29669285
DOI: 10.1016/j.celrep.2018.03.099
call_split See protocol

[…] tween −1 kb and +1 kb of the TSSs using the ‘intersect’ tool in the bedtools software (v2.26.0). MSCS2 (v2.2.1) was used for the peak calling. For further analyses and visualization, ngsplot (v2.41), ChIPpeakAnno (v3.5), Homer (v4.9), and Integrative Genome Viewer (v2.3.91) were used. Sequences of qPCR primers for ChIP-qPCR are as follows: Prdm1 forward (fwd): CCAGTAGGCCTTT CATGGCT, Prdm1 reverse […]

library_books

DNA methylation profiles correlated to striped bass sperm fertility

2018
BMC Genomics
PMCID: 5894188
PMID: 29636007
DOI: 10.1186/s12864-018-4548-6

[…] on. After creating a contrast between conditions, the R package DiffBind runs an edgeR analysis with a false discovery rate (FDR) < 0.1 to call the differentially methylated regions (DMRs). Then, the ChIPpeakAnno package was used for the genomic annotation of the previously identified DMRs. This software provides information about the distance, relative position, and overlaps for the inquired feat […]

library_books

Cryptic glucocorticoid receptor binding sites pervade genomic NF κB response elements

2018
Nat Commun
PMCID: 5889392
PMID: 29626214
DOI: 10.1038/s41467-018-03780-1

[…] motif with a score of 90% or greater, as determined using the Biostrings package in Bioconductor. For Gene Ontology analyses, the nearest transcription start site to each peak was determined with the ChIPpeakAnno package and results input to the DAVID ontology server. […]

Citations

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ChIPpeakAnno institution(s)
Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA; UMR217 CNRS/CEA, iRCM-CEA, Evry, France; Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; The Biomedical Informatics Center, Northwestern University, Chicago, IL, USA; Information Services, University of Massachusetts Medical School, Worcester, MA, USA
ChIPpeakAnno funding source(s)
Supported by the Program in Gene Function and Expression (PGFE) at UMass Medical School (UMMS).

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