A software package for the differential RNA methylation analysis at small sample size scenario from MeRIP-Seq data. The proposed model can effectively describe within-group biological variability at small sample size scenario and handles the impact of transcriptional regulation on RNA methylation. We tested the newly developed DRME algorithm on simulated and 4 MeRIP-Seq case-control studies and compared it with Fisher's exact test. It is in principle widely applicable to several other RNA-related data types as well, including RNA Bisulfite sequencing and PAR-CLIP.
Predicts differential m6A methylation sites from Methylated RNA immunoprecipitation sequencing (MeRIP-Seq) data. MeTDiff consists of two major steps: (1) determining and statistical modeling putative differentially m6A sites; (2) and significance test for the inferred regions. For the first step, it determines the putative differential m6A methylation sites (DMSs) to be tested for differential methylation. And for the second step, it computes the statistical significance using a likelihood ratio test.
Allows users to analyze differential RNA methylation. QNB is based on four negative binomial distributions with their means and variances crosslinked together. This tool proceeds an analysis thanks to the small-sample sequencing data. Its model can also be applied to other data types related to RNA modifications, such as RNA bisulfite sequencing, RIP-Seq, Par-CLIP and m1 A-Seq.