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. |