MethylSeekR protocols

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MethylSeekR specifications

Information


Unique identifier OMICS_00607
Name MethylSeekR
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 1.20.0
Stability Stable
Requirements
rtracklayer(>=1.16.3), parallel(>=2.15.1), mhsmm(>=0.4.4), IRanges(>=1.16.3), BSgenome(>=1.26.1), GenomicRanges(>=1.10.5), geneplotter(>=1.34.0), graphics(>=2.15.2), grDevices(>=2.15.2), parallel(>=2.15.2), stats(>=2.15.2), utils(>=2.15.2), BSgenome.Hsapiens.UCSC.hg18
Maintained Yes

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Publication for MethylSeekR

MethylSeekR in pipeline

2017
PMCID: 5522596
PMID: 28732548
DOI: 10.1186/s13059-017-1273-4

[…] were removed using prinseq []. the read mapping to the reference genome and methylation base calling was performed using bs-seeker2 []. the lumrs were identified for both cg and chg data using methylseekr []. the threshold for percent methylation for the low methylated regions (lmrs) was set to 20%. methylseekr [] defines unmethylated regions (umrs) and lmrs; in this study, we combined […]


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MethylSeekR in publications

 (14)
PMCID: 5756049
PMID: 29267285
DOI: 10.1371/journal.pgen.1007102

[…] from ucsc (https://genome.ucsc.edu). cpg islands were retrieved from ucsc (“cpgislandext” table) using rtracklayer []. unmethylated (umrs) and low-methylated regions (lmrs) were determined using methylseekr [] on esc and np whole-genome bisulfite data [] with parameters m = 50% and n = 3 (smallest n such that fdr < 5%) as previously described []. lmrs were further subdivided […]

PMCID: 5522596
PMID: 28732548
DOI: 10.1186/s13059-017-1273-4

[…] were removed using prinseq []. the read mapping to the reference genome and methylation base calling was performed using bs-seeker2 []. the lumrs were identified for both cg and chg data using methylseekr []. the threshold for percent methylation for the low methylated regions (lmrs) was set to 20%. methylseekr [] defines unmethylated regions (umrs) and lmrs; in this study, we combined […]

PMCID: 5353786
PMID: 28302063
DOI: 10.1186/s12864-017-3617-6

[…] reads, in eq. (), we obtained the combined number of methylated reads at k. after collecting these numbers, we had a combined methylation profile for each tested sample class. we then applied methylseekr [] to each combined methylation profile with the setting of chr.sel = chr2, meth.cutoff = 0.5 and ncpg.cutoff = 3. at the end, we established a map of consensus dres, together with sres […]

PMCID: 5389478
PMID: 27899585
DOI: 10.1093/nar/gkw1110

[…] or prepared from the gencode hg19 annotation by methods similar to those described in; https://www.gitbook.com/book/ycl6/methylation-sequencing-analysis. hypomethylated regions were identified using methylseekr () and overlapping hypomethylated regions were determined using the ‘findoverlaps’ function in the r package genomicranges using default settings ()., a low complexity tag of varying […]

PMCID: 5080608
PMID: 27782217
DOI: 10.1038/srep35903

[…] that may provide evidence to explain the phenomenon of sexual size dimorphism. using the wgbs data generated for tilapia, we inferred the acrs from the hybrid tilapia genome using the software methylseekr. we generated a biostrings-based r library, bsgenome.oniloticus.ucsc.orenil2, as the reference genome for methylseekr analysis. a methylation cutoff point of 50% and a false discovery […]


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MethylSeekR institution(s)
Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland, Swiss Institute of Bioinformatics, Basel, Switzerland; University of Basel, Basel, Switzerland

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