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Repitools specifications

Information


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
Requirements
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

Subtool


  • BayMeth

Download


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Versioning


No version available

Documentation


Maintainer


  • person_outline Mark Robinson

Publications for Repitools

Repitools citations

 (12)
library_books

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

2016
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, […]

library_books

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

2016
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 […]

library_books

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

2015
FEBS Lett
PMCID: 4686001
PMID: 26619763
DOI: 10.1016/j.febslet.2015.11.027

[…] /peakSeq/optimal/hub/. Bam files for the corresponding experiments were downloaded from https://www.encodeproject.org/, 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 […]

call_split

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

2015
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 (http://bioconductor.org/packages/release/bioc/html/Repitools.html - settings: ipWidth = 100, inputWidth = 500 and preset =“large”) []. For identifying regions that were enriched for a speci […]

call_split

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

2015
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 (). […]

library_books

Coordinated epigenetic remodelling of transcriptional networks occurs during early breast carcinogenesis

2015
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 […]

Citations

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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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