RgnTX: Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity.

ABSTRACT: Colocalization analysis of genomic region sets has been widely adopted to unveil potential functional interactions between corresponding biological attributes, which often serves as the basis for further investigation. A number of methods have been developed for colocalization analysis of genomic elements. However, none of them explicitly considered the transcriptome heterogeneity and isoform ambiguity, making them less appropriate for analyzing transcriptome elements. Here, we developed RgnTX, an R/Bioconductor tool for the colocalization analysis of transcriptome elements with permutation tests. Different from existing approaches, RgnTX directly takes advantage of transcriptome annotation, and offers high flexibility in the null model to simulate realistic transcriptome-wide background,

SUBMITTER: Wang Y 

PROVIDER: S-EPMC10475473 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature