Man pages for haowulab/TRESS
Toolbox for mRNA epigenetics sequencing analysis
| Basal | Bin-level and region-level data from basal mouse brain... |
| CallCandidates | Call candidate m6A regions or candidate differential m6A... |
| CallDMRs.paramEsti | Model fitting and parameter estimation by TRESS for each... |
| 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... |
| 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,... |
| 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... |
| TRESS_DMRtest | Hypothesis testing on candidate DMRs. |
| TRESS_peak | Detecting m6A methylation regions from Methylated RNA... |
