MeRIP-seq data analysis bioinformatics software tools

MeRIP-seq analysis steps

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 data analysis bioinformatics software tools

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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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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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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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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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