Toolbox for mRNA epigenetics sequencing analysis

Documentation for package ‘TRESS’ version 1.6.0

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.