CBAF: An automated and easy-to-use R package for comparing genetics data across multiple cancers/ a cancer’s subgroups

Bioconductor is a repository of open-source packages written in R programming language to fulfill the needs of biologists. CBAF is a Bioconductor package that enables the researchers to compare at least one groups of genes across several cancers / cancer’s subgroups that are available at cbioportal.org. So far, it is compatible with RNA sequencing (RNA-Seq), microRNA sequencing (microRNA-Seq), microarray, and methylation data.There is a function that scans all the cancers in cbioportal.org to identify which of the mentioned high-throughput technique exists for every cancer. Two other functions automatically obtain, process and store the results. They require at least one group of gene names, any desired name to title the created database, name of cancer(s), and the desired technique. Firstly, they obtain the required data from cbioportal.org. Then, they compute the required statistics such as frequency percentage and mean value of samples having a value greater than a specific number. Moreover, they determine the genes that occupy the first to fifth rank in every section.The output is prepared as one heatmap for every statistical measurement and a multi-section excel file that contains the result of validating genes on the cbioportal, numerical values of requested statistics and the genes that occupy the first to fifth rank in every category. If more than one groups of genes are requested, the output for every gene group is stored in a separate folder. To sum up, this easy-to-use package is recommended to all biologists.

Keywords:

R , Bioconductor , RNA-Seq , microRNA-Seq , Microarray , Methylation