methylPipe protocols

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methylPipe specifications

Information


Unique identifier OMICS_06799
Name methylPipe
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 1.14.0
Stability Stable
Requirements
methods, stats, gplots, parallel, graphics, BiocGenerics, IRanges, GenomicRanges, Rsamtools, utils, S4Vectors, GenomeInfoDb, Biostrings, grDevices, GenomicAlignments, Gviz, data.table, marray, R(>=3.2.0), SummarizedExperiment(>=0.2.0)
Maintained Yes

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Publication for methylPipe

methylPipe in pipeline

2016
PMCID: 4926291
PMID: 27358654
DOI: 10.1186/s13072-016-0075-3

[…] that enables a correction for multiple testing., schmitz et al. performed a large-scale wgbs analysis in which dmrs from many arabidopsis methylomes were detected []. they used the r package methylpipe to scan the genome with 100-bp windows [], and the methylation level of the sites within a window was compared across all samples using a kruskal–wallis test. the p values […]


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methylPipe in publications

 (4)
PMCID: 5719354
PMID: 29215068
DOI: 10.1038/s41598-017-17460-5

[…] fig. ). the 4 clusters had 7209, 7277, 6878 and 2275 genes, separately, of which the mean expression level of cluster 4 was significantly lower than other clusters (supplementary fig. )., using methylpipe, dmrs between ck and le (ck_vs_le), between ck and he (ck_vs_he), and between he and le (le_vs_he) were identified. a total of 4,941, 2,563 and 6047 dmrs were identified for ck_vs_he, […]

PMCID: 5135077
PMID: 27932863
DOI: 10.2147/DDDT.S116192

[…] for hh3r in nanomo-lar concentration range (ki: 27–156 nm). for the tested group of novel h3r ligands, among four different cycloalkylamine moieties used (piperidine, 3-methylpiperidine, 4-methylpipe-ridine, homopiperidine), it is obvious that 3-methylpiperidine is the most preferable basic moiety for hh3r binding pocket. interestingly, 3-methylpiperidine derivative 6 with hh3r ki […]

PMCID: 4926291
PMID: 27358654
DOI: 10.1186/s13072-016-0075-3

[…] users studying other organisms should take the flexibility of the tools into account. the accommodation of different data types should also be considered, e.g., biseq supports rrbs only, whereas methylpipe supports rrbs and wgbs, as well as low-resolution dna methylation data., this review provides an overview of the current techniques for the assessment of genome-wide dna methylation […]

PMCID: 3337477
PMID: 22540040
DOI: 10.1534/g3.111.001362

[…] phusion taq included in the nebnext kit using the following pcr conditions (2 min at 95°, 4 cycles of 15 sec at 98°, 30 sec at 60°, 4 min at 72°, and 10 min at 72°)., dmrs were identified using the methylpipe package in r (; pelizzola, unpublished results). each specific methylation context (cg, chg, and chh) was scanned genome-wide requiring at least 10 mc differences within a 100 bp window. […]


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methylPipe institution(s)
Center for Genomic Science of IITASEMM, Istituto Italiano di Tecnologia (IIT), Milano, Italy; Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, Australia; Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA; Department of Experimental Oncology, European Institute of Oncology (IEO), Milano, Italy; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA

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