PRIME gathers a suite of R functions for:

• analyzing transcription start site (TSS) data, e.g. CAGE, or other RNA 5' end data like GRO/PRO-cap
• analyzing divergent transcription
• calling enhancers and promoters from TSS data
• subsampling of data, e.g. for saturation analyses
• decomposition of TSS clusters for core promoter analysis
• calculation of genomic background (noise) expression
• normalization across libraries
• dealing with experimental batches

The R package PRIME depends on a mix of CRAN, Bioconductor, and GitHub packages. Please refer to Installation instructions for details.

• PRIMEprep Preprocessing and mapping of CAGE sequencing data. Recommended to prepare data for PRIME analysis.
• PRIMEloci Prediction of regulatory elements from transcription initiation data.

• Robin Andersson
• Natsuda Navamajiti
• Hjorleifur Einarsson
• Robert Krautz
• Nicolas Alcaraz