pliu55 / pram

An R/Bioconductor package to predict intergenic transcript models from RNA-seq

PRAM: Pooling RNA-seq and Assembling Models

Table of Contents

• Introduction
• Installation
• Reference
• Contact
• License

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Introduction

Pooling RNA-seq and Assembling Models (PRAM) is an Bioconductor R package that utilizes multiple RNA-seq datasets to predict transcript models. The workflow of PRAM contains four steps, which is shown in the figure below with function names and associated key parameters. PRAM has a vignette that describes each function in details.

Installation

From GitHub

Start R and enter:

devtools::install_github('pliu55/pram')

From Bioconductor

Start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("pram")

Reference

PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments. Peng Liu, Alexandra A. Soukup, Emery H. Bresnick, Colin N. Dewey, and Sündüz Keleş. Genome Research 2020. 30:1655-1666

For key results reported in the PRAM manuscript and scripts for reproducibility, please check out this GitHub repository.

Contact

Got a question? Please report it at the issues tab in this repository.

License

PRAM is licensed under the GNU General Public License v3.