Repitools protocols

View Repitools computational protocol

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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

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Documentation


Maintainer


  • person_outline Mark Robinson <>

Publications for Repitools

Repitools in pipeline

2015
PMCID: 4660036
PMID: 25728682
DOI: 10.1038/onc.2015.24

[…] project (geo accession gse19465). samples gsm621634 and gsm773000 (adult kidney) were analysed using sample gsm621638 (adult kidney) as input control. peaks were called using chromablocks from the repitools package, using ‘small' as preset and a fdr cut-off of 0.1. h3k36me3 sites were defined as the overlap between peaks from samples gsm621634 and gsm7733000. h3k27me3 sites were similarly […]


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Repitools in publications

 (11)
PMCID: 5828078
PMID: 29482641
DOI: 10.1186/s40478-018-0519-z

[…] differentially-methylated gene promoters (5000 bp upstream and 200 bp downstream from the transcription start site), exons, and gene body area were identified with blocksstats function in the repitools 1.21.1 r package [] with r version 3.1.0. the adjusted p-value was calculated with a benjamini–hochberg false discovery rate (fdr). dna methylation was considered significantly changed […]

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

[…] 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 […]

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

[…] methylated regions (dmrs) between rwpe-1 and 22rv1 cells (fold change >1, fdr < 0.1)., 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 […]

PMCID: 4499136
PMID: 26007656
DOI: 10.1093/nar/gkv508

[…] 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 ()., the chipseq, the rnaseq and the microarray data from this publication have been submitted to the geo […]

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

[…] 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 […]


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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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