CINmetrics: An R package for chromosomal instability analysis
Oza, V. H.; Fisher, J. L.; Darji, R.; Lasseigne, B. N.
Show abstract
Genomic instability is an important hallmark of cancer and more recently has been identified in others like neurodegenrative diseases. Chromosomal instability, as a measure of genomic instability, has been used to characterize clinical and biological phenotypes associated with these diseases by measuring structural and numerical chromosomal alterations. There have been multiple chromosomal instability scores developed across many studies in the literature; however, these scores have not been compared because of the lack of a single tool available to calculate and facilitate these various metrics. Here, we provide an R package CINmetrics, that calculates six different chromosomal instability scores and allows direct comparison between them. We also demonstrate how these scores differ by applying CINmetrics to breast cancer data from The Cancer Genome Atlas (TCGA). The package is available on CRAN at https://cran.r-project.org/package=CINmetrics and on github at https://github.com/lasseignelab/CINmetrics.
Matching journals
The top 3 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- A comprehensive algorithmic dissection yields biomarker discovery and insights into the discrete stage-wise progression of colorectal cancer 91%
- Automated evaluation of multiple sequence alignment methods to handle third generation sequencing errors 90%
- High-performance pipeline for MutMap and QTL-seq 89%
Similar papers in this journal
- Benchmarking software tools for trimming adapters and merging next-generation sequencing data for ancient DNA 91%
- Functional networks of the human bromodomain-containing proteins 89%
- An assessment of bioinformatics tools for the detection of human endogenous retroviral insertions in short-read genome sequencing data 88%
Similar papers in this journal
- Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions 91%
- CANCERSIGN: a user-friendly and robust tool for identification and classification of mutational signatures and patterns in cancer genomes 91%
- RBV: Read balance validator, a tool for prioritising copy number variations in germline conditions 91%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.