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CMARRT specifications

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Unique identifier OMICS_18712
Name CMARRT
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 1.3
Stability Stable
Source code URL http://www.ams.sunysb.edu/~pfkuan/CMARRT/CMARRT_1.3.tar.gz
Maintained Yes

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Publication for CMARRT

CMARRT citations

 (8)
library_books

Impact of Anaerobiosis on Expression of the Iron Responsive Fur and RyhB Regulons

2015
MBio
PMCID: 4676285
PMID: 26670385
DOI: 10.1128/mBio.01947-15

[…] previously described (). chip and input data were quantile normalized using “normalize.quantiles” from the preprocesscore package () in r (), and enriched binding regions were identified using the cmarrt peak-calling algorithm (p < 0.1) (). enriched regions were removed from the final chip-seq peak list if they were also present in the fur− strain data., rna was isolated from two biological […]

library_books

Effects of Low Dose Diethylstilbestrol Exposure on DNA Methylation in Mouse Spermatocytes

2015
PLoS One
PMCID: 4654501
PMID: 26588706
DOI: 10.1371/journal.pone.0143143

[…] and control group, we can calculate the ratio between experiment group and control group, the absolute methylation level and relative methylation levels of each promoter in each sample. we used the cmarrt algorithm to calculate the enrichment region of the probe peak, the value p was calculated by the gauss distribution. and then the promoter region of the gene was annotated, the annotation […]

library_books

Prenatal stress induced programming of genome wide promoter DNA methylation in 5 HTT deficient mice

2014
PMCID: 4350514
PMID: 25335169
DOI: 10.1038/tp.2014.107

[…] quantile normalization was applied to the signal log2 ratios, followed by a 300 bp sliding-window median smoothing. autosomal regions enriched by the medip procedure were detected by the cmarrt algorithm. with the present (=1) and absent (=0) calls for medip enrichment, effect directions were determined as previously described. briefly, genotype (g) effect directions (d) […]

library_books

The Cavβ1a subunit regulates gene expression and suppresses myogenin in muscle progenitor cells

2014
PMCID: 4068134
PMID: 24934157
DOI: 10.1083/jcb.201403021

[…] tbe gels., the average log2 (cavβ1a/igg) intensity value of the two biological replicates was computed for each probe position. regions enriched for cavβ1a relative to igg were determined using cmarrt () on the average log2 (cavβ1a/igg) at the fdr level of 0.05. peak annotation, distance to tss, and position to nearest gene were performed using chippeakanno () and the galaxy web platform (; […]

library_books

Genome scale Analysis of Escherichia coli FNR Reveals Complex Features of Transcription Factor Binding

2013
PLoS Genet
PMCID: 3688515
PMID: 23818864
DOI: 10.1371/journal.pgen.1003565

[…] was a strong correlation between enriched regions of chip-chip biological replicates (r = 0.7). chip-chip peaks for fnr, h-ns and ihf were identified in each data set by the peak finding algorithm cmarrt, version 1.3 (fdr of 0.01) and proportional z-tests were used to determine significant differences between proportional data., for chip-seq experiments, 10 ng of immunoprecipitated […]

library_books

DNA Methylation Mediated Control of Gene Expression Is Critical for Development of Crown Gall Tumors

2013
PLoS Genet
PMCID: 3567176
PMID: 23408907
DOI: 10.1371/journal.pgen.1003267

[…] of the two groups were then subjected to a 500 bp sliding window median smoothing in order to create a robust and smoothed slr (sslr) for each probe position in each group. an implementation of the cmarrt algorithm , was used for detection of genomic regions with consistently increased sslrs across at least five consecutive probes for each of the two groups. for all regions displaying signal […]


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CMARRT institution(s)
Department of Statistics, University of Wisconsin, Madison, WI, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA
CMARRT funding source(s)
Supported in part by a PhARMA Foundation Research Starter Grant and NIH grants 1-R01-HG03747-01 and 4-R37-GM038660-20.

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