Toolbox for mRNA epigenetics sequencing analysis


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Documentation for package ‘TRESS’ version 1.6.0

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Basal Bin-level and region-level data from basal mouse brain samples
CallCandidates Call candidate m6A regions or candidate differential m6A regions.
CallDMRs.paramEsti Model fitting and parameter estimation by TRESS for each candidate DMR.
CallPeaks.multiRep m6A peak calling with multiple replicates.
CallPeaks.oneRep m6A peak calling with only one replicate.
CallPeaks.paramEsti Parameter estimation in m6A peak calling with multiple replicates.
CoefName Obtain the name of each coefficient in design matrix.
DivideBins Obtain genomic bins and bin-level read counts from BAM files.
DMRInfer P-value calculation given Wald statistics.
DMR_M3vsWT Transcriptome location and read counts of 200 candidate DMRs, and size factors.
DMR_SixWeekvsTwoWeek Transcriptome location and read counts of 200 candidate DMRs.
filterRegions Pre-filtering of candidate DMRs.
findBumps Bump-finding from transcriptome bins.
meRatio Observed m6A methylation ratio.
ShowOnePeak Visulization of a single peak along the genome.
TRESS_DMRfit Differential m6A methylation analysis for MeRIP-seq data under general experimental design
TRESS_DMRtest Hypothesis testing on candidate DMRs.
TRESS_peak Detecting m6A methylation regions from Methylated RNA Immunoprecipitation Sequencing.