Biocview "CopyNumberVariation"

Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing

A Hidden Markov Model for high throughput genotyping arrays

Analysis of Copy Number Variation in Single-Cell-Sequencing Data

An integrated analysis package of Gene expression and Copy number alteration

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

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

A normalization method for Copy Number Aberration in cancer samples

An R package for copy number data segmentation

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

A RangedSummarizedExperiment with methods for copy number analysis

A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling

A Software Suite for Shallow Sequencing Copy Number Analysis

Assessment of evidence for LOH in spatial transcriptomics pre-processed data using Bayes factor calculations

Association analysis of genomic regions based on permutation tests

Bayesian mixture models for copy number polymorphisms

Bayesian mixture models for copy number polymorphisms long running unit tests

Bayesian Piecewise Constant Regression for DNA copy number estimation

Bioconductor components for general cancer genomics

BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data

Candidate gene prioritization based on convergent evidence

CGHbase: Base functions and classes for arrayCGH data analysis.

CGH Micro-Array NORmalization

Characterising single circulating tumor cell transcriptomes

Chromosome Instability Index

Classes and functions for Array Comparative Genomic Hybridization data

cn.FARMS - factor analysis for copy number estimation

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

CNproScan detects and annotates CNVs in bacterial genomes.

CNV detection tool for targeted NGS panel data

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

CommunityAMARETTO: A Computational Tool for the Discovery of Shared and Distinct Regulatory Mechanisms Across Biological Systems

Comparing tumour copy number profiles

Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data

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

Copy Number Analysis for 450k Illumina Methylation Arrays

Copy number analysis of high-throughput sequencing cancer data

Copy number calling and SNV classification using targeted short read sequencing

Copy number data analysis using DNA sequencing data

Copy number information from ChIP_seq using off-target reads off-target reads

Copy number information from targeted sequencing using off-target reads

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

Copy Number study and Segmentation for multivariate biological data

Copy number variant detection from exome sequencing read depth

Copy Number Variant Metrics

Copy Number Visualization

Create Copy-Number Plots using karyoploteR functionality

Delineate outstanding genomic zones of differential gene activity

Dimension Reduction for Array CGH Data with Minimal Information Loss.

DNA copy number data analysis

DNA Copy Number Data Analysis

DNA IP-seq data analysis

Enhanced copy-number variation analysis using Illumina DNA methylation arrays

fastseg - a fast segmentation algorithm

Feature-based association and gene-set enrichment for copy number alteration analysis in cancer

Find chromosome regions showing common gains/losses

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

GAIA: An R package for genomic analysis of significant chromosomal aberrations.

Gain and Loss Analysis of DNA

Gene Break Detection

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

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

Get CNV information from 450K array

Identifies false positives of CNV calling tools by using SNV calls

ImagingAMARETTO: tools for interpreting multi-omics networks for relevance to clinical outcomes and radiographic and histopathology imaging-derived biomarkers

Implementation of wave correction for arrays

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

Integrated Copy Number Variation detection

Integrative analysis of multi-omics data to infer regulatory networks

Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

IP-seq data analysis and vizualization

ITALICS

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

Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data

Multilevel Model for Multivariate Responses with Missing Values

Multi-Omics integration and VIsualization in Cancer Subtyping

Multi sample aCGH analysis package using kernel convolution

NGScopy: Detection of Copy Number Variations in Next Generation Sequencing sequencing

Normalization and reporting of Illumina SNP bead arrays

Outlier Gene Set Analysis

Plot customizable linear genomes displaying arbitrary data

Position Related Data Analysis

Pre-process DNA Copy Number (CN) Data for Detection of CN Events

Processing Various Types of Data on GEO and TCGA

Quantile smoothing and genomic visualization of array data

Quantitative DNA Sequencing for Chromosomal Aberrations

rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines

Refitting diploid region profiles using a clustering procedure

Regional Expression Biases

Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression

Reliable CNV detection in targeted sequencing applications

R package for calling CNV from Illumina 450k methylation microarrays

R wrapper for Progenetix

sciCNV

Secondary analyses of CNV data (HRD and more)

Segmentation, normalisation and processing of aCGH data

Segmentation of single- and multi-track copy number data by penalized least squares regression.

Segmentation of single- and multi-track copy number data by penalized least squares regression (with hg38 and mm10).

Subclonal copy number and LOH prediction from whole genome sequencing of tumours

Summarization and expression/phenotype association of CNV ranges

svpluscnv: analysis and visualization of complex structural variation data

Tumor subclonality of expression-based cancer subtypes

Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression

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

Visualizations for copy number alterations

Biocview "CopyNumberVariation"

R Package Documentation

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