Biocview "CopyNumberVariation"

Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing
Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing
A Hidden Markov Model for high throughput genotyping arrays
A Hidden Markov Model for high throughput genotyping arrays
Analysis of Copy Number Variation in Single-Cell-Sequencing Data
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 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 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
Association analysis of genomic regions based on permutation tests
Association analysis of genomic regions based on permutation tests
Bayesian mixture models for copy number polymorphisms
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
Bayesian Piecewise Constant Regression for DNA copy number estimation
Bioconductor components for general cancer genomics
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
Candidate gene prioritization based on convergent evidence
Candidate gene prioritization based on convergent evidence
Candidate gene prioritization based on convergent evidence
CGHbase: Base functions and classes for arrayCGH data analysis.
CGHbase: Base functions and classes for arrayCGH data analysis.
CGH Micro-Array NORmalization
Chromosome Instability Index
Classes and functions for Array Comparative Genomic Hybridization data
cn.FARMS - factor analysis for copy number estimation
cn.FARMS - factor analysis for copy number estimation
cn.mops - Mixture of Poissons for CNV detection in NGS data
CNV detection tool for targeted NGS panel data
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
Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data
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 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 information from targeted sequencing using off-target reads
Copy number prediction with correction for GC and mappability bias for HTS data
Copy number prediction with correction for GC and mappability bias for HTS data
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
Create Copy-Number Plots using karyoploteR functionality
Create Copy-Number Plots using karyoploteR functionality
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
DNA IP-seq data analysis
DNA IP-seq data analysis
DNA IP-seq 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
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
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
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
Infer Copy Number Variation from Single-Cell RNA-Seq Data
Infer Copy Number Variation from Single-Cell RNA-Seq Data
Integrated Copy Number Variation detection
Integrated Copy Number Variation detection
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
IP-seq data analysis and vizualization
IP-seq data analysis and vizualization
ITALICS
Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data
Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data
Multilevel Model for Multivariate Responses with Missing Values
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
Plot customizable linear genomes displaying arbitrary data
Position Related Data Analysis
Pre-process DNA Copy Number (CN) Data for Detection of CN Events
Quantile smoothing and genomic visualization of array data
Quantitative DNA Sequencing for Chromosomal Aberrations
Quantitative DNA Sequencing for Chromosomal Aberrations
rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines
rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines
rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines
Regional Expression Biases
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
Reliable CNV detection in targeted sequencing applications
Reliable CNV detection in targeted sequencing applications
Reliable CNV detection in targeted sequencing applications
R package for calling CNV from Illumina 450k methylation microarrays
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.
Subclonal copy number and LOH prediction from whole genome sequencing of tumours
Subclonal copy number and LOH prediction from whole genome sequencing of tumours
Subclonal copy number and LOH prediction from whole genome sequencing of tumours
Summarization and expression/phenotype association of CNV ranges
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
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