CNTools

CNTools converts DNAcopy segmented genomic output into a matrix representing overlapping genomic segments as rows and samples as columns to enable copy number variation (CNV) and other downstream computational analyses.

Key Features:

• Data Conversion: Parses DNAcopy segmentation output and structures overlapping genomic segments as rows and samples as columns in a matrix suitable for computational analysis.
• Interoperability with Bioconductor: Produces R/Bioconductor-compatible data structures to enable downstream use with other Bioconductor packages and workflows.

Scientific Applications:

• Matrix preparation for downstream analysis: Provides a consolidated matrix representation of segmented data for inputs to clustering, statistical testing, and visualization methods.
• Copy number variation (CNV) analysis: Facilitates comparative analysis of segment overlaps across samples to support CNV detection and interpretation.
• Clustering and differential analysis: Enables application of clustering and differential analysis methods on reorganized segmented data to identify sample groups and segment-level differences.

Methodology:

Implemented in R, CNTools parses DNAcopy segmentation output and organizes overlapping genomic segments into a sample-by-segment matrix.