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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

Versioning


No version available

Documentation


Publication for MethylSeekR

MethylSeekR citations

 (14)
library_books

Binding of high mobility group A proteins to the mammalian genome occurs as a function of AT content

2017
PLoS Genet
PMCID: 5756049
PMID: 29267285
DOI: 10.1371/journal.pgen.1007102

[…] aded 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 into ESC-specific […]

library_books

Genome wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize

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

[…] imming 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 both […]

library_books

Epigenetic and genetic alterations and their influence on gene regulation in chronic lymphocytic leukemia

2017
BMC Genomics
PMCID: 5353786
PMID: 28302063
DOI: 10.1186/s12864-017-3617-6

[…] hylated 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 an […]

library_books

SPlinted Ligation Adapter Tagging (SPLAT), a novel library preparation method for whole genome bisulphite sequencing

2016
Nucleic Acids Res
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 (). […]

library_books

Genome wide methylation analysis identified sexually dimorphic methylated regions in hybrid tilapia

2016
Sci Rep
PMCID: 5080608
PMID: 27782217
DOI: 10.1038/srep35903

[…] lation of methylation profiles across various repeat elements.MethylSeekR was used to infer regulatory element landscape in the R-environment. Biostrings-based reference genome data were required for MethylSeekR, but was unavailable for the Nile tilapia reference genome as it is not a model species. Hence, a Biostrings-based R library, BSgenome.Oniloticus.UCSC.oreNil2.tar.gz, was created for oreNi […]

library_books

Epigenetic dynamics of monocyte to macrophage differentiation

2016
PMCID: 4967341
PMID: 27478504
DOI: 10.1186/s13072-016-0079-z

[…] the 650–700 million read pairs per sample was executed by bwa [] version 0.7.5a and a modified human reference (hs37d5) to achieve C/T-tolerance. The segmentation into LMRs and UMRs was performed by MethylSeekR [] version 1.6.0 with a FDR cutoff of 0.05. An in-house script was used to call the CpG methylation levels, excluding reads with a mapping quality lower than 30 (probability to map at a co […]

Citations

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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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