Tool sets to analyze high throughput data for RNA modifications
Depends: GenomicFeatures, Rsamtools, ggplot2, doParallel, foreach,grid,rtracklayer,GenomicAlignments,reshape2,Rcpp,RcppArmadillo, Guitar, stringr,vcfR,gamlss, broom, DESeq2
install.packages("devtools")
library(devtools)
install_github("scottzijiezhang/MeRIPtools")
library("MeRIPtools")Please refer to manual page for detailed instructions.
MeRIPtools is a tool sets that implemented functions for peak calling, QTL calling, differential methylation analysis, visualization.
If you used MeRIPtools in your publication, please cite: Zhang, Z., Luo, K., Zou, Z. et al. Genetic analyses support the contribution of mRNA N6-methyladenosine (m6A) modification to human disease heritability. Nat Genet 52, 939–949 (2020). https://doi.org/10.1038/s41588-020-0644-z
Note MeRIPtools also have wrapper functions to call functions from other R packages to do specific analysis.
If you used the plotMetaGene or MetaGene function, please cite the original R package Guitar
Cui X, Wei Z, Zhang L, Liu H, Sun L, Zhang s, Huang Y, Meng J (2016). “Guitar: an R/Bioconductor package for gene annotation guided transcriptomic analysis of RNA related genomic features.” BioMed Research International.