ccp2tools

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Overview

ccp2tools provides utility functions for analyzing circRNA expression data generated by the CirComPara2 pipeline.
It simplifies importing results into R and combining multiple CirComPara2 runs or projects.

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Installation

From Bioconductor

install.packages("BiocManager")
BiocManager::install("remotes")
BiocManager::install("egaffo/ccp2tools")

Using renv

renv::install("egaffo/ccp2tools")

Main Features

• combine_ccp2_runs(): Import and merge multiple CirComPara2 projects.
• to_summarized_experiment(): Extract expression estimates and into a SummarizedExperiment object.

Quick Start

combine_ccp2_runs {#combine_ccp2_runs}

combine_ccp2_runs() makes it easy to import the results of CirComPara2 into an R environment.
In addition, it allows combining multiple CirComPara2 projects or runs. For instance, when you split your dataset into multiple batches to be processed with CirComPara2, or you use ccp2_nf, the Nextflow interface to run CirComPara2.

Basic usage:

library(ccp2tools)
prjs <- c("/home/user/circompara2/samples_batch1",
           "/home/user/circompara2/samples_batch2")

combined_prjs <- combine_ccp2_runs(prjs)

For more details:

?combine_ccp2_runs

to_summarized_experiment {#to_summarized_experiment}

to_summarized_experiment() allows the extraction of the cirRNA, gene, or transcript expression estimates from the result of calling the combine_ccp2_runs function, returning a SummarizedExperiment object for downstream analysis.

Basic usage:

library(ccp2tools)
prjs <- c("/home/user/circompara2/samples_batch1",
           "/home/user/circompara2/samples_batch2")

combined_prjs <- combine_ccp2_runs(prjs)

circ_se <- to_summarized_experiment(combined_prjs)

For more details:

?to_summarized_experiment