Bioconductor Packages

Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing

Analysis of Big Data from aCGH Experiments using Parallel Computing and ff Objects

Refitting diploid region profiles using a clustering procedure

CGHbase: Base functions and classes for arrayCGH data analysis.

Dimension Reduction for Array CGH Data with Minimal Information Loss.

A normalization method for Copy Number Aberration in cancer samples

Convert segment data into a region by sample matrix to allow for other high level computational analyses.

Copy Number Variant Metrics

Reliable CNV detection in targeted sequencing applications

Summarization and expression/phenotype association of CNV ranges

Identifies false positives of CNV calling tools by using SNV calls

Copy Number Visualization

CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.

A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing

Create Copy-Number Plots using karyoploteR functionality

DNA Copy Number Data Analysis

An R Package for Estimating Copy Number Levels of Viral Genome Segments Using Base-Resolution Read Depth Profile

Gain and Loss Analysis of DNA

Gene Break Detection

Delineate outstanding genomic zones of differential gene activity

Processing Various Types of Data on GEO and TCGA

Copy number prediction with correction for GC and mappability bias for HTS data

ITALICS

Multi sample aCGH analysis package using kernel convolution

MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data

CGH Micro-Array NORmalization

DNA IP-seq data analysis

A Package for De Novo CNV Detection in Case-Parent Trios

Position Related Data Analysis

Copy number calling and SNV classification using targeted short read sequencing

Quantitative DNA Sequencing for Chromosomal Aberrations

A normalization and copy number estimation method for single-cell DNA sequencing

A Hidden Markov Model for high throughput genotyping arrays

VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer

Classes and functions for Array Comparative Genomic Hybridization data

Call CNV from single cell ATAC-seq data based on InferCNV adaptation

Copy Number study and Segmentation for multivariate biological data

Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA)

Find chromosome regions showing common gains/losses

cn.FARMS - factor analysis for copy number estimation

cn.mops - Mixture of Poissons for CNV detection in NGS data

Enhanced copy-number variation analysis using Illumina DNA methylation arrays

Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays

Efficient Gene Set Enrichment Analysis for DNA Methylation Data

fastseg - a fast segmentation algorithm

Multi-Omics data integration

Integrated Copy Number Variation detection

An integrated analysis package of Gene expression and Copy number alteration

Infer Copy Number Variation from Single-Cell RNA-Seq Data

Plot customizable linear genomes displaying arbitrary data