GitHub - pliu55/pram: An R/Bioconductor package to predict intergenic transcript models from RNA-seq (original) (raw)

PRAM: Pooling RNA-seq and Assembling Models

Table of Contents

• Introduction
• Installation
• Reference
• Contact
• License

Introduction

Pooling RNA-seq and Assembling Models (PRAM) is an Bioconductor Rpackage 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 avignette 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 outthis 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.