Getting Started with the PRIME Toolkit

Overview

The PRIME toolkit consists of three interconnected tools for the analysis of transcription initiation data (e.g., CAGE):

Tool	Type	Purpose
PRIMEprep	Bash pipeline	Raw FASTQ → QC → trimming → mapping → BigWig
PRIME	R package	CTSS quantification, divergent loci, promoter decomposition, normalization, noise estimation
PRIMEmodel	R package + Python	Genome-wide prediction of regulatory elements

The tools form a linear pipeline, and CAGEfightR provides core CTSS data structures that PRIME extends:

FASTQ files
    │
    ▼
┌───────────┐
│ PRIMEprep │  Shell: QC → trim → rRNA filter → STAR map → G-correction → BigWig
└────┬──────┘
     │ BigWig files (plus/minus strand)
     ▼
┌──────────┐
│  PRIME   │  R package (extends CAGEfightR)
│          │  ● quantify CTSSs (via CAGEfightR)
│          │  ● pool replicates, subsample, normalize
│          │  ● call tag clusters & divergent loci
│          │  ● decompose promoters
│          │  ● estimate noise
│          │  ● complexity & saturation analysis
└────┬─────┘
     │ CTSS RangedSummarizedExperiment objects
     ▼
┌────────────┐
│ PRIMEmodel │  R package + Python (LightGBM)
│            │  ● genome-wide prediction of regulatory elements
│            │  ● focal prediction on defined regions
│            │  ● post-processing & BED output
└────────────┘

Installation

1. Bioconductor dependencies (CAGEfightR)

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

2. PRIME

if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")
devtools::install_github("anderssonlab/PRIME")

PRIME depends on a mix of CRAN, Bioconductor, and GitHub packages. See the detailed installation guide: vignette("installation") or articles/installation.html.

3. PRIMEmodel (requires Python >= 3.9)

devtools::install_github("anderssonlab/PRIMEmodel")

PRIMEmodel requires a Python environment (>= 3.9) with LightGBM and supporting packages. See the detailed installation guide: vignette("primemodel-installation") or articles/primemodel-installation.html.

4. PRIMEprep

PRIMEprep is a shell-based preprocessing pipeline. Clone the repository:

git clone https://github.com/anderssonlab/PRIMEprep.git

PRIMEprep depends on the following external tools (recommended versions):

Tool	Version
STAR	v2.7.3a
fastp	v0.23.4
samtools	v1.20.0
rRNAdust	v1.02
bedGraphToBigWig	v4.0
preseq	v2.0
FastQC	v0.12.1
bedtools	v2.31.0
Perl	v5.38.0
openjdk	v20.0.0