PRIME '

PRIME - regulatory element analysis using transcription start site data

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 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 versus GC content
• calculation of bias in expression coverage and expression support versus batch

Installation:

Install PRIME directly from GitHub using devtools:

devtools::install_github("anderssonlab/PRIME")

You may need to manually install dependencies (See DESRIPTION).

Notes:

• PRIME uses CAGEfightR as a base for data loading and handling
• R package bcp is not vailable from CRAN for R >= 4.3. To install bcp, use install_github("swang87/bcp")

Contributors

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

TO DO

• write vignettes

Future development

• ATAC-CAGE integration
• QC tools and visualization