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
Maintainer
License`use_gpl3_license()`
Version0.9.0
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("remotes")
remotes::install_github("Maxim-Ivanov/TranscriptomeReconstructoR")
Maxim-Ivanov/TranscriptomeReconstructoR documentation built on Jan. 28, 2021, 11:47 a.m.