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ChIPQC specifications


Unique identifier OMICS_13398
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 3.0
Computer skills Advanced
Version 1.16.0
Stability Stable
methods, stats, Biobase, utils, BiocStyle, grDevices, ggplot2, BiocParallel, DiffBind, GenomicFeatures, gtools, R(>=3.0.0), reshape2, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Mmusculus.UCSC.mm10.knownGene, Nozzle.R1, BiocGenerics(>=0.11.3), GenomicRanges(>=1.17.19), Rsamtools(>=1.17.28), GenomicAlignments(>=1.1.16), TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, S4Vectors(>=0.1.0), IRanges(>=1.99.17), chipseq(>=1.12.0), TxDb.Celegans.UCSC.ce6.ensGene
Maintained Yes


  • Invertebrates
    • Caenorhabditis elegans
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus




No version available



  • person_outline Rory Stark
  • person_outline Tom Carroll
  • person_outline Ines de Santiago

Publication for ChIPQC

ChIPQC citations


NOTCH mediated non cell autonomous regulation of chromatin structure during senescence

Nat Commun
PMCID: 5943456
PMID: 29743479
DOI: 10.1038/s41467-018-04283-9

[…] contaminations were filtered using Cutadapt (version 1.10.0), and reads mapping to the ‘blacklisted’ regions identified by ENCODE were further removed. Average fragment size was determined using the ChIPQC Bioconductor package, and peak calling was performed with MACS2 (version 2.1.0), using fragment size as an extension size (--extsize) parameter. High-confidence peak sets for each condition wer […]


Gene specific mechanisms direct glucocorticoid receptor driven repression of inflammatory response genes in macrophages

PMCID: 5821458
PMID: 29424686
DOI: 10.7554/eLife.34864.026

[…] nomic Workbench (GR, Pol 2) or bowtie2 (p65, NELF-E, BRD4). Aligned BAM files were converted into bigwig format for data visualization purposes. The quality of Chip-seq experiments was assessed using ChIPQC package () (). Cross-correlation analysis, Relative Strand Correlation (RSC) and Normalized Strand Cross-correlation coefficient (NSC) for all ChIP-seq datasets used in this study were calculat […]


Prenatal Exposure to a Maternal High Fat Diet Affects Histone Modification of Cardiometabolic Genes in Newborn Rats

PMCID: 5409746
PMID: 28425976
DOI: 10.3390/nu9040407

[…] lling algorithm for broad binding regions. The called peaks were annotated to the nearest TSS (Transcript Starting Site) using ChIPpeakAnno, version 3.2.0 []. ChIP quality control was performed using ChIPQC, version 1.2.2 []. Raw nucleotide sequences are available in the National Center for Biotechnology Information (NCBI) gene expression omnibus database under the accession number GSE84831. […]


A high resolution map of transcriptional repression

PMCID: 5373822
PMID: 28318487
DOI: 10.7554/eLife.22767.036

[…] , aligned, sorted and indexed with samtools version 0.1.18. Duplicate reads were marked using Picard MarkDuplicates. The quality of the datasets and predicted fragment lengths were analysed using the ChIPQC Bioconductor package. Normalised BigWig files were generated using rtracklayer (version 1.3.2) with signal normalised to total mapped fragments per sample. ChIP-seq sample quality was assessed […]


Neonatal monocytes exhibit a unique histone modification landscape

Clin Epigenetics
PMCID: 5028999
PMID: 27660665
DOI: 10.1186/s13148-016-0265-7
call_split See protocol

[…] ) was performed on an Illumina HiSeq machine, resulting in 10–20 million reads/sample. The quality of samples was assessed using FastQC ( and ChIPQC []. All samples passed quality control measures, which are outlined in Additional file : Table S14. […]


A FOXM1 Dependent Mesenchymal Epithelial Transition in Retinal Pigment Epithelium Cells

PLoS One
PMCID: 4488273
PMID: 26121260
DOI: 10.1371/journal.pone.0130379

[…] were aligned to the human genome (GRCh37 via Ensembl release 72) using BWA. Peaks were identified using MACS v1.4.2. Downstream processing was performed in R using the Bioconductor packages DiffBind, ChIPQC and Gviz. Gene Ontology terms and associations were taken from Bioconductor annotation packages Go.db and Motif enrichment was performed using MEME. ChIPseq raw data are available […]


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ChIPQC institution(s)
Cambridge Institute CRUK, University of Cambridge, Cambridge, UK; Lymphocyte Development, MRC Clinical Sciences Centre, Imperial College, London, UK

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