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Repitools specifications


Unique identifier OMICS_00619
Name Repitools
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.26.0
Stability Stable
methods, gplots, parallel, grid, GenomicRanges, Rsamtools, DNAcopy, GenomeInfoDb, ShortRead, Biostrings, rtracklayer, GenomicAlignments, BSgenome.Hsapiens.UCSC.hg18, MASS, R(>=3.0.0), BiocGenerics(>=0.8.0), S4Vectors(>=0.17.25), IRanges(>=2.13.12), BSgenome(>=1.47.3), gsmoothr, edgeR(>=3.4.0), Ringo, aroma.affymetrix, Rsolnp, cluster
Maintained Yes


  • BayMeth




No version available



  • person_outline Mark Robinson

Publications for Repitools

Repitools citations


Genomic agonism and phenotypic antagonism between estrogen and progesterone receptors in breast cancer

Sci Adv
PMCID: 4928895
PMID: 27386569
DOI: 10.1126/sciadv.1501924

[…] ributions for analysis. Differential binding in ChIP-seq was analyzed using the DiffBind R package. Receptor binding heat maps for ChIP were plotted 5 kb up- and downstream of the ChIP peak using the Repitools R package. An overlap of at least 1 bp was considered to determine whether two different ChIP peaks were overlapping. Investigations of ChIP peak overlaps were performed using GenomicRanges, […]


Dynamic interplay between locus specific DNA methylation and hydroxymethylation regulates distinct biological pathways in prostate carcinogenesis

Clin Epigenetics
PMCID: 4791926
PMID: 26981160
DOI: 10.1186/s13148-016-0195-4

[…] Sequenced reads were mapped to the reference human genome (GRCh37, hg19) using Bowtie (v0.12.7) []. Repitools package [] was used as an enrichment diagnostic screen of sequenced samples, enriched and input. Significantly enriched regions/peaks of hydroxymethylation were determined using model-based […]


Variable reproducibility in genome scale public data: A case study using ENCODE ChIP sequencing resource

PMCID: 4686001
PMID: 26619763
DOI: 10.1016/j.febslet.2015.11.027

[…] /peakSeq/optimal/hub/. Bam files for the corresponding experiments were downloaded from, and merged using Samtools . The mean coverages around peaks were computed using Repitools . Statistically significant differentially bound regions were identified using MAnorm with a 150 base pair read shift. Peaks were annotated with the closest TSS using bedtools and GENCODE v […]


cChIP seq: a robust small scale method for investigation of histone modifications

BMC Genomics
PMCID: 4687106
PMID: 26692029
DOI: 10.1186/s12864-015-2285-7
call_split See protocol

[…] --ignoreDuplicates). For H3K4me1 and H3K4me3, peaks were called using MACS v1.4 using the --nomodel mode []. For H3K27me3, domains (broad peaks) were called using ChromaBlocks [] using the R package Repitools ( - settings: ipWidth = 100, inputWidth = 500 and preset =“large”) []. For identifying regions that were enriched for a speci […]


Dynamics of MBD2 deposition across methylated DNA regions during malignant transformation of human mammary epithelial cells

Nucleic Acids Res
PMCID: 4499136
PMID: 26007656
DOI: 10.1093/nar/gkv508
call_split See protocol

[…] ). K-mean clusterization of peaks and subsequent visualization were performed with seqMINER (). Integrative analysis of ChIPseq, RNAseq and ChIP-chip data was performed using the Bioconductor package Repitools (). Top enriched motifs in peaks were obtained using the RSAT oligo-diff tool (). […]


Coordinated epigenetic remodelling of transcriptional networks occurs during early breast carcinogenesis

Clin Epigenetics
PMCID: 4424562
PMID: 25960784
DOI: 10.1186/s13148-015-0086-0

[…] l analysis and Model-based Analysis of Tiling arrays (MAT) normalisation of ChIP-chip data was performed using aroma.affymetrix []. Array signal across all promoters on the array was determined using Repitools [,,]. ChIP data was then summarised to a t-statistic for a region of ±2 kb of all transcription start sites (TSS) with the function blocksStats []. Regions of LRER were identified by the met […]


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Repitools institution(s)
Epigenetics Laboratory, Cancer Program, Garvan Institute of Medical Research, Darlinghurst, NSW Australia; St Vincent’s Clinical School, The University of New South Wales, NSW, Australia; Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, VIC, Australia
Repitools funding source(s)
Supported by National Health and Medical Research Council (NH&MRC) project (427614, 481347) and Fellowship, Cancer Institute NSW grants and NBCF Program Grant.

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