MethPipe statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Bioinformatics workflows Read alignment Bisulfite conversion rate estimation Methylation scoring Differentially methylated region detection Allele-specific DNA methylation detection chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

MethPipe specifications

Information


Unique identifier OMICS_00603
Name MethPipe
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input format FASTQ, BAM, SAM
Output format BAM, tab-delimited text
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 3.3.1
Stability Stable
Maintained Yes

Versioning


Add your version

Documentation


Maintainer


  • person_outline Andrew Smith <>

Publication for MethPipe

MethPipe in publications

 (12)
PMCID: 5870497
PMID: 29580210
DOI: 10.1186/s12864-018-4594-0

[…] by assessing number of unconverted cytosines that aligned to the lambda genome from the lambda spike-in control and assessment of typically unmethylated cyotsines across the genome using the methpipe software [] (details: additional file : table s5)., cytosines that had an average coverage across all samples of 5 or more reads and displayed at least 10% methylation levels in three […]

PMCID: 5752839
PMID: 29076502
DOI: 10.1038/cr.2017.134

[…] (version: 0.16.3; parameter settings: “bismark --pbat -n 1 -l 40”). potential pcr duplicates were removed using the deduplicate bismark command., post-alignment analysis was performed by using the methpipe package. first, aligned sequences were converted to methpipe format using the to-mr command. methylation levels and coverage for each symmetric cpg site were calculated by the methcounts […]

PMCID: 5655803
PMID: 29065907
DOI: 10.1186/s13059-017-1335-7

[…] at reference cytosine positions in the lambda genome. see below for sequencing and conversion statistics., dna-methylation free (hypo-methylated) regions were detected using the hmr tool from methpipe version 3.0.0 (http://smithlabresearch.org/software/methpipe/) [], to consider a region as actively transcribed, we measured the h3k36me3 and rnapii marks (as rpkm) of 200,000 random regions […]

PMCID: 5138066
PMID: 27980397
DOI: 10.4137/BBI.S38427

[…] kernel smoothing (dmr-cate), nonparametric and kernel-based method (m3d), beta-binomial model (methylsig), beta-binomial hierarchical model (moabs), hidden markov model (nhmmfdr), three-state hmm (methpipe), shannon entropy (qdmr), and a binary segmentation algorithm combined with a two-dimensional statistical test (metilene). usually, the latest software compares with some previous methods […]

PMCID: 4896262
DOI: 10.1186/s13167-016-0054-6

[…] setup genome- and immunome-wide biomarker-discovery as well a targeted technologies using multiplexed technologies for validation of these markers. combining the relevant technologies we call these methpipe and peppipe for enabling us streamlined biomarker-development for dna-methylation and antibody-based diagnostics., results interpretation: plasma derived cell free dna methylation maker […]


To access a full list of publications, you will need to upgrade to our premium service.

MethPipe institution(s)
Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA

MethPipe reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review MethPipe