MeRIP-seq data analysis bioinformatics software tools

RNA modifications, especially methylation of the N6 position of adenosine (m6A), represent an emerging research frontier in RNA biology. Along with the development of MeRIP-Seq (Meyer et al., 2012) also called m6A-seq (Dominissini et al., 2012), researchers are knowable to carry…

MeRIP-seq analysis steps

MeRIP-seq data analysis bioinformatics software tools

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Guitar
Desktop

Guitar

A package for sketching the transcriptomic view of RNA-related biological…

A package for sketching the transcriptomic view of RNA-related biological features represented by genome based coordinates. Guitar extracts the standardized RNA coordinates with respect to the…

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MeTPeak
Desktop

MeTPeak

A graphical model-based peak calling method for transcriptome-wide detection of…

A graphical model-based peak calling method for transcriptome-wide detection of m6A sites from MeRIP-seq data. MeTPeak models read count of m6A site and introduces a hierarchical layer of Beta…

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ExomePeak
Desktop

ExomePeak

The package is developed for the analysis of affinity-based epitranscriptome…

The package is developed for the analysis of affinity-based epitranscriptome shortgun sequencing data from MeRIP-seq (maA-seq).

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MeTCluster
Desktop

MeTCluster

An R package for uncovering the potential types of m6A methylation by…

An R package for uncovering the potential types of m6A methylation by clustering the degree of m6A methylation peaks in MeRIP-Seq data. This algorithm utilizes a hierarchical graphical model to model…

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DRME
Desktop

DRME Differential RNA MEthylation

A software package for the differential RNA methylation analysis at small…

A software package for the differential RNA methylation analysis at small sample size scenario from MeRIP-Seq data. The proposed model can effectively describe within-group biological variability at…

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HEPeak
Desktop

HEPeak

A hidden Markov model (HMM)-based Exome Peak-finding algorithm for predicting…

A hidden Markov model (HMM)-based Exome Peak-finding algorithm for predicting transcriptome methylation sites using MeRIP-seq data. By introducing the exome-based annotation, HEPeak circumvents the…

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MeRIP-PF
Desktop

MeRIP-PF MeRIP-Seq Peak-Finding Program

A high-efficiency and easy-to-use analysis pipeline for MeRIP-Seq peak-finding…

A high-efficiency and easy-to-use analysis pipeline for MeRIP-Seq peak-finding at high resolution, which compares distributions of reads between immunoprecipitation sample and control sample.

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QNB
Desktop

QNB Quadratic Negative Binomial

A tool for differential methylation analysis. QNB estimates variance and mean…

A tool for differential methylation analysis. QNB estimates variance and mean dependence in count data from MeRIP-seq and test for differential methylation based on a model using…

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