# Toolbox for mRNA epigenetics sequencing analysis

## Documentation for package ‘TRESS’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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.