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.
Start R and enter:
devtools::install_github('pliu55/pram')
Start R and enter:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("pram")
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.
Got a question? Please report it at the issues tab in this repository.
PRAM is licensed under the GNU General Public License v3.
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