Maxim-Ivanov/TranscriptomeReconstructoR: Data-driven Annotation of the Transcriptome

This package reconstructs the most probable gene/transcript model for a species by combining a few orthogonal high throughput sequencing datasets. The three essential datasets are as follows: i) 5' tag RNA sequencing dataset which shows TSS (transcription start sites), e.g. CAGE; ii) 3' tag RNA sequencing dataset which shows PAS (polyadenylation sites); iii) Full-length RNA sequencing dataset which shows splicing patterns (e.g. Direct RNA-seq on Oxford Nanopore). Optionally, a nascent RNA-seq dataset (e.g. NET-seq or GRO-seq) can be added to resolve the transient non-coding transcripts.

Getting started

Package details

Bioconductor views Annotation GenomeBrowsers Sequencing Software Transcription Transcriptomics
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
Maxim-Ivanov/TranscriptomeReconstructoR documentation built on Jan. 28, 2021, 11:47 a.m.