ChIPpeakAnno protocols

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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

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Publication for ChIPpeakAnno

ChIPpeakAnno in pipelines

 (18)
2018
PMCID: 5889392
PMID: 29626214
DOI: 10.1038/s41467-018-03780-1

[…] 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., approximately 106 a549 cells cultured in complete dulbecco’s modified eagle’s medium (dmem) were transfected with 2 μg pcdna3.1 […]

2017
PMCID: 5305219
PMID: 28191871
DOI: 10.7554/eLife.22474.039

[…] duplicates., to identify regions enriched with reads when compared to an input control we used macs () (q-value 0.05). peaks were annotated in terms of distance to nearest gene (user-defined) using chippeakanno (bioconductor) (). we associated smad2-binding loci to the closest differential gene as determined by our rna-seq and chip-seq for pol ii ser5 data (max distance 100 kb from tss/tts). […]

2017
PMCID: 5599894
PMID: 28911330
DOI: 10.1186/s13059-017-1302-3

[…] tfs using the drem framework []. to decrease the size of the tf–gene interaction dataset [], we kept the strongest 25% peaks for each of the 287 tfs and identified their presumed target with chippeakanno []. only associations with a p value < 10−7 are shown. tf binding data, gene expression data, parameters and output model used in drem modelling are shown in additional file : sd3., […]

2017
PMCID: 5791885
PMID: 28991266
DOI: 10.1038/nsmb.3481

[…] expressed genes were identified with the limma and selected with a cut-off of a q-value of 0,05 calculated after false discovery rate correction. the gene ontology analysis was performed using chippeakanno r package using p-value < 0.01 and 30 for mingoterm (minimum count in a genome for a go term to be included). a bonferroni multiple hypothesis testing adjustment was finally applied […]

2016
PMCID: 4891180
PMID: 27178982
DOI: 10.7554/eLife.12717.044

[…] in the microarray 1000 times and assuming a normal distribution. annotation of binding events and association with genomic features was performed with peakanalyzer () and the r/bioconductor package chippeakanno ()., postnatal brains collected at p7 and p15 were fixed by immersion in 4% paraformaldehyde at 4°c for overnight followed by cryoprotection in pbs containing 30% sucrose. histological […]


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ChIPpeakAnno in publications

 (115)
PMCID: 5940187
PMID: 29738565
DOI: 10.1371/journal.pone.0196965

[…] 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 […]

PMCID: 5923282
PMID: 29704004
DOI: 10.1038/s41598-018-24915-w

[…] 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., chipseq data have been deposited […]

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 […]

PMCID: 5947873
PMID: 29669285
DOI: 10.1016/j.celrep.2018.03.099

[…] −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 […]

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

[…] 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 […]


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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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