bioconductor.org "CopyNumberVariation" keyword
View the packages on the bioconductor.org package registry that are tagged with the "CopyNumberVariation" keyword.
Top 2.2% on bioconductor.org
6 versions - Latest release: about 1 month ago - 13 dependent packages - 261 thousand downloads total - 1 maintainer
regioneR 1.40.1
Association analysis of genomic regions based on permutation tests6 versions - Latest release: about 1 month ago - 13 dependent packages - 261 thousand downloads total - 1 maintainer
tLOH 1.16.0
Assessment of evidence for LOH in spatial transcriptomics pre-processed data using Bayes factor c...5 versions - Latest release: 3 months ago - 6.48 thousand downloads total - 3 stars on GitHub - 1 maintainer
ELViS 1.0.0
An R Package for Estimating Copy Number Levels of Viral Genome Segments Using Base-Resolution Rea...1 version - Latest release: 3 months ago - 1.18 thousand downloads total - 0 stars on GitHub - 1 maintainer
aCGH 1.86.0
Classes and functions for Array Comparative Genomic Hybridization data5 versions - Latest release: 3 months ago - 5 dependent packages - 71.6 thousand downloads total - 1 maintainer
Top 3.8% on bioconductor.org
5 versions - Latest release: 3 months ago - 1 dependent package - 115 thousand downloads total - 1 maintainer
fastseg 1.54.0
fastseg - a fast segmentation algorithm5 versions - Latest release: 3 months ago - 1 dependent package - 115 thousand downloads total - 1 maintainer
Top 7.1% on bioconductor.org
5 versions - Latest release: 3 months ago - 27 thousand downloads total - 87 stars on GitHub - 1 maintainer
TitanCNA 1.45.0
Subclonal copy number and LOH prediction from whole genome sequencing of tumours5 versions - Latest release: 3 months ago - 27 thousand downloads total - 87 stars on GitHub - 1 maintainer
Top 2.9% on bioconductor.org
6 versions - Latest release: 21 days ago - 8 dependent packages - 106 thousand downloads total - 318 stars on GitHub - 1 maintainer
karyoploteR 1.34.2
Plot customizable linear genomes displaying arbitrary data6 versions - Latest release: 21 days ago - 8 dependent packages - 106 thousand downloads total - 318 stars on GitHub - 1 maintainer
CopyNumberPlots 1.24.0
Create Copy-Number Plots using karyoploteR functionality6 versions - Latest release: about 2 months ago - 2 dependent packages - 13.9 thousand downloads total - 6 stars on GitHub - 1 maintainer
MAGAR 1.16.0
MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation an...5 versions - Latest release: 2 months ago - 8.23 thousand downloads total - 0 stars on GitHub - 1 maintainer
pgxRpi 1.4.3
R wrapper for Progenetix11 versions - Latest release: about 1 month ago - 3.86 thousand downloads total - 3 stars on GitHub - 1 maintainer
gINTomics 1.4.0
Multi-Omics data integration3 versions - Latest release: 2 months ago - 2.62 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 5.0% on bioconductor.org
5 versions - Latest release: 3 months ago - 6 dependent packages - 85.6 thousand downloads total - 0 stars on GitHub - 1 maintainer
CGHbase 1.68.0
CGHbase: Base functions and classes for arrayCGH data analysis.5 versions - Latest release: 3 months ago - 6 dependent packages - 85.6 thousand downloads total - 0 stars on GitHub - 1 maintainer
CNVfilteR 1.22.0
Identifies false positives of CNV calling tools by using SNV calls6 versions - Latest release: about 2 months ago - 9.37 thousand downloads total - 5 stars on GitHub - 1 maintainer
AneuFinder 1.35.0
Analysis of Copy Number Variation in Single-Cell-Sequencing Data5 versions - Latest release: 3 months ago - 35.4 thousand downloads total - 18 stars on GitHub - 1 maintainer
conumee 1.42.0
Enhanced copy-number variation analysis using Illumina DNA methylation arrays5 versions - Latest release: 3 months ago - 30.4 thousand downloads total - 1 maintainer
rCGH 1.38.0
Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data5 versions - Latest release: 3 months ago - 1 dependent package - 20.9 thousand downloads total - 4 stars on GitHub - 1 maintainer
CODEX 1.40.0
A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing5 versions - Latest release: 3 months ago - 1 dependent package - 28.6 thousand downloads total - 1 maintainer
Top 4.7% on bioconductor.org
6 versions - Latest release: 3 months ago - 117 thousand downloads total - 615 stars on GitHub - 1 maintainer
infercnv 1.24.0
Infer Copy Number Variation from Single-Cell RNA-Seq Data6 versions - Latest release: 3 months ago - 117 thousand downloads total - 615 stars on GitHub - 1 maintainer
VegaMC 3.46.0
VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver ...5 versions - Latest release: 3 months ago - 25.9 thousand downloads total - 1 maintainer
CINdex 1.36.0
Chromosome Instability Index5 versions - Latest release: 3 months ago - 15.8 thousand downloads total - 1 maintainer
CNVMetrics 1.12.0
Copy Number Variant Metrics5 versions - Latest release: 3 months ago - 5.45 thousand downloads total - 4 stars on GitHub - 1 maintainer
regioneReloaded 1.10.0
RegioneReloaded: Multiple Association for Genomic Region Sets5 versions - Latest release: 3 months ago - 4.87 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 6.0% on bioconductor.org
5 versions - Latest release: 3 months ago - 3 dependent packages - 61.6 thousand downloads total - 1 maintainer
cn.mops 1.54.0
cn.mops - Mixture of Poissons for CNV detection in NGS data5 versions - Latest release: 3 months ago - 3 dependent packages - 61.6 thousand downloads total - 1 maintainer
Top 4.3% on bioconductor.org
6 versions - Latest release: 3 months ago - 3 dependent packages - 78.1 thousand downloads total - 3 maintainers
crlmm 1.66.0
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumin...6 versions - Latest release: 3 months ago - 3 dependent packages - 78.1 thousand downloads total - 3 maintainers
rcellminer 2.30.0
rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines5 versions - Latest release: 3 months ago - 20.4 thousand downloads total - 3 maintainers
sparsenetgls 1.26.0
Using Gaussian graphical structue learning estimation in generalized least squared regression for...5 versions - Latest release: 3 months ago - 9.08 thousand downloads total - 1 maintainer
Top 9.1% on bioconductor.org
5 versions - Latest release: 3 months ago - 33.6 thousand downloads total - 1 maintainer
KCsmart 2.66.0
Multi sample aCGH analysis package using kernel convolution5 versions - Latest release: 3 months ago - 33.6 thousand downloads total - 1 maintainer
CNVRanger 1.24.2
Summarization and expression/phenotype association of CNV ranges7 versions - Latest release: about 2 months ago - 13 thousand downloads total - 4 stars on GitHub - 1 maintainer
MinimumDistance 1.52.1
A Package for De Novo CNV Detection in Case-Parent Trios6 versions - Latest release: about 2 months ago - 27.9 thousand downloads total - 1 maintainer
SARC 1.6.0
Statistical Analysis of Regions with CNVs4 versions - Latest release: 3 months ago - 3.91 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 4.2% on bioconductor.org
5 versions - Latest release: 3 months ago - 5 dependent packages - 92.2 thousand downloads total - 1 maintainer
GLAD 2.72.0
Gain and Loss Analysis of DNA5 versions - Latest release: 3 months ago - 5 dependent packages - 92.2 thousand downloads total - 1 maintainer
VanillaICE 1.70.1
A Hidden Markov Model for high throughput genotyping arrays7 versions - Latest release: about 2 months ago - 2 dependent packages - 46.8 thousand downloads total - 1 maintainer
iCNV 1.28.0
Integrated Copy Number Variation detection5 versions - Latest release: 3 months ago - 12 thousand downloads total - 1 maintainer
BubbleTree 2.38.0
BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic m...5 versions - Latest release: 3 months ago - 21 thousand downloads total - 2 maintainers
Top 5.4% on bioconductor.org
5 versions - Latest release: 3 months ago - 4 dependent packages - 60.4 thousand downloads total - 50 stars on GitHub - 1 maintainer
QDNAseq 1.44.0
Quantitative DNA Sequencing for Chromosomal Aberrations5 versions - Latest release: 3 months ago - 4 dependent packages - 60.4 thousand downloads total - 50 stars on GitHub - 1 maintainer
Top 8.9% on bioconductor.org
5 versions - Latest release: 3 months ago - 35.2 thousand downloads total - 1 maintainer
ITALICS 2.68.0
ITALICS5 versions - Latest release: 3 months ago - 35.2 thousand downloads total - 1 maintainer
AMARETTO 1.24.0
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis an...5 versions - Latest release: 3 months ago - 14.2 thousand downloads total - 1 maintainer
Top 9.2% on bioconductor.org
5 versions - Latest release: 3 months ago - 1 dependent package - 39.3 thousand downloads total - 1 maintainer
CGHregions 1.66.0
Dimension Reduction for Array CGH Data with Minimal Information Loss.5 versions - Latest release: 3 months ago - 1 dependent package - 39.3 thousand downloads total - 1 maintainer
Top 5.0% on bioconductor.org
5 versions - Latest release: 3 months ago - 1 dependent package - 74.7 thousand downloads total - 1 maintainer
HMMcopy 1.50.0
Copy number prediction with correction for GC and mappability bias for HTS data5 versions - Latest release: 3 months ago - 1 dependent package - 74.7 thousand downloads total - 1 maintainer
Top 8.3% on bioconductor.org
5 versions - Latest release: 3 months ago - 36.6 thousand downloads total - 1 maintainer
MANOR 1.80.0
CGH Micro-Array NORmalization5 versions - Latest release: 3 months ago - 36.6 thousand downloads total - 1 maintainer
MADSEQ 1.34.0
Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data5 versions - Latest release: 3 months ago - 13.9 thousand downloads total - 4 stars on GitHub - 1 maintainer
BOBaFIT 1.12.0
Refitting diploid region profiles using a clustering procedure5 versions - Latest release: 3 months ago - 5.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
GeneBreak 1.38.0
Gene Break Detection5 versions - Latest release: 3 months ago - 16.4 thousand downloads total - 2 stars on GitHub - 1 maintainer
GeoTcgaData 2.8.0
Processing Various Types of Data on GEO and TCGA5 versions - Latest release: 3 months ago - 6.23 thousand downloads total - 26 stars on GitHub - 1 maintainer
Top 5.5% on bioconductor.org
5 versions - Latest release: 3 months ago - 54.5 thousand downloads total - 1 maintainer
MEDIPS 1.60.0
DNA IP-seq data analysis5 versions - Latest release: 3 months ago - 54.5 thousand downloads total - 1 maintainer
CNVrd2 1.46.0
CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from...5 versions - Latest release: 3 months ago - 26.9 thousand downloads total - 3 stars on GitHub - 1 maintainer
GenomicOZone 1.22.0
Delineate outstanding genomic zones of differential gene activity5 versions - Latest release: 3 months ago - 9.18 thousand downloads total - 1 maintainer
CNVPanelizer 1.40.0
Reliable CNV detection in targeted sequencing applications5 versions - Latest release: 3 months ago - 19.8 thousand downloads total - 1 maintainer
SCOPE 1.20.0
A normalization and copy number estimation method for single-cell DNA sequencing5 versions - Latest release: 3 months ago - 8.74 thousand downloads total - 1 maintainer
CNViz 1.16.0
Copy Number Visualization5 versions - Latest release: 3 months ago - 6.02 thousand downloads total - 1 maintainer
Top 2.0% on bioconductor.org
5 versions - Latest release: 3 months ago - 29 dependent packages - 686 thousand downloads total - 1 maintainer
DNAcopy 1.82.0
DNA Copy Number Data Analysis5 versions - Latest release: 3 months ago - 29 dependent packages - 686 thousand downloads total - 1 maintainer
ACE 1.26.0
Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing5 versions - Latest release: 3 months ago - 14.8 thousand downloads total - 15 stars on GitHub - 1 maintainer
PureCN 2.14.1
Copy number calling and SNV classification using targeted short read sequencing8 versions - Latest release: 2 months ago - 32.3 thousand downloads total - 134 stars on GitHub - 1 maintainer
Top 9.9% on bioconductor.org
5 versions - Latest release: 3 months ago - 30.9 thousand downloads total - 1 maintainer
mBPCR 1.62.0
Bayesian Piecewise Constant Regression for DNA copy number estimation5 versions - Latest release: 3 months ago - 30.9 thousand downloads total - 1 maintainer
CNAnorm 1.54.0
A normalization method for Copy Number Aberration in cancer samples5 versions - Latest release: 3 months ago - 31.5 thousand downloads total - 1 maintainer
Top 9.6% on bioconductor.org
5 versions - Latest release: 3 months ago - 31.4 thousand downloads total - 1 maintainer
PREDA 1.54.0
Position Related Data Analysis5 versions - Latest release: 3 months ago - 31.4 thousand downloads total - 1 maintainer
qsea 1.34.0
IP-seq data analysis and vizualization5 versions - Latest release: 3 months ago - 15.4 thousand downloads total - 1 maintainer
cn.farms 1.55.0
cn.FARMS - factor analysis for copy number estimation5 versions - Latest release: 3 months ago - 41.1 thousand downloads total - 1 maintainer
cfdnakit 1.6.0
Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA)5 versions - Latest release: 3 months ago - 4.19 thousand downloads total - 6 stars on GitHub - 1 maintainer
panelcn.mops 1.30.0
CNV detection tool for targeted NGS panel data5 versions - Latest release: 3 months ago - 1 dependent package - 14.8 thousand downloads total - 1 maintainer
Top 5.8% on bioconductor.org
5 versions - Latest release: 3 months ago - 1 dependent package - 61.5 thousand downloads total - 1 maintainer
CNTools 1.64.0
Convert segment data into a region by sample matrix to allow for other high level computational a...5 versions - Latest release: 3 months ago - 1 dependent package - 61.5 thousand downloads total - 1 maintainer
partCNV 1.6.0
Infer locally aneuploid cells using single cell RNA-seq data4 versions - Latest release: 3 months ago - 3.84 thousand downloads total - 1 maintainer
biomvRCNS 1.48.0
Copy Number study and Segmentation for multivariate biological data6 versions - Latest release: 3 months ago - 27.3 thousand downloads total - 1 maintainer
Top 6.2% on bioconductor.org
5 versions - Latest release: 3 months ago - 56.3 thousand downloads total - 1 maintainer
cghMCR 1.66.0
Find chromosome regions showing common gains/losses5 versions - Latest release: 3 months ago - 56.3 thousand downloads total - 1 maintainer
Top 3.3% on bioconductor.org
5 versions - Latest release: 3 months ago - 4 dependent packages - 117 thousand downloads total - 1 maintainer
quantsmooth 1.74.0
Quantile smoothing and genomic visualization of array data5 versions - Latest release: 3 months ago - 4 dependent packages - 117 thousand downloads total - 1 maintainer
pathwayPCA 1.24.0
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection5 versions - Latest release: 3 months ago - 1 dependent package - 11.6 thousand downloads total - 11 stars on GitHub - 1 maintainer
IntOMICS 1.4.0 removed
Integrative analysis of multi-omics data to infer regulatory networks3 versions - Latest release: about 1 year ago - 1.07 thousand downloads total - 0 stars on GitHub - 1 maintainer
BiocOncoTK 1.26.0 removed
Bioconductor components for general cancer genomics5 versions - Latest release: 8 months ago - 13.4 thousand downloads total - 1 maintainer
iGC 1.36.0
An integrated analysis package of Gene expression and Copy number alteration4 versions - Latest release: 8 months ago - 13.3 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 9.5% on bioconductor.org
3 versions - Latest release: about 1 year ago - 38.5 thousand downloads total - 1 maintainer
beadarraySNP 1.70.0 removed
Normalization and reporting of Illumina SNP bead arrays3 versions - Latest release: about 1 year ago - 38.5 thousand downloads total - 1 maintainer
Top 8.8% on bioconductor.org
3 versions - Latest release: about 1 year ago - 27.4 thousand downloads total - 1 maintainer
SMAP 1.68.0 removed
A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling3 versions - Latest release: about 1 year ago - 27.4 thousand downloads total - 1 maintainer
seqCNA 1.48.0 removed
Copy number analysis of high-throughput sequencing cancer data2 versions - Latest release: over 1 year ago - 1 dependent package - 18.5 thousand downloads total - 1 maintainer
snapCGH 1.72.0 removed
Segmentation, normalisation and processing of aCGH data2 versions - Latest release: over 1 year ago - 2 dependent packages - 41.8 thousand downloads total - 1 maintainer
CopywriteR 2.32.0 removed
Copy number information from targeted sequencing using off-target reads1 version - Latest release: almost 2 years ago - 18.3 thousand downloads total - 28 stars on GitHub - 1 maintainer
Top 5.4% on bioconductor.org
2 versions - Latest release: over 1 year ago - 3 dependent packages - 52.2 thousand downloads total - 1 maintainer
exomeCopy 1.48.0 removed
Copy number variant detection from exome sequencing read depth2 versions - Latest release: over 1 year ago - 3 dependent packages - 52.2 thousand downloads total - 1 maintainer
Top 5.2% on bioconductor.org
1 version - Latest release: almost 2 years ago - 1 dependent package - 57 thousand downloads total - 1 maintainer
copynumber 1.40.0 removed
Segmentation of single- and multi-track copy number data by penalized least squares regression.1 version - Latest release: almost 2 years ago - 1 dependent package - 57 thousand downloads total - 1 maintainer
oncoscanR 1.6.0
Secondary analyses of CNV data (HRD and more)3 versions - Latest release: about 1 year ago - 3.04 thousand downloads total - 2 stars on GitHub - 1 maintainer
Related Keywords
Software
77
Sequencing
32
Microarray
27
Visualization
22
Genetics
19
Coverage
14
DNASeq
13
Preprocessing
13
SNP
13
GenomicVariation
13
GeneExpression
12
DataImport
10
Normalization
10
QualityControl
9
aCGH
9
ImmunoOncology
9
DNAMethylation
8
WholeGenome
8
Clustering
6
DifferentialExpression
6
TwoChannel
6
DifferentialMethylation
5
HiddenMarkovModel
5
Transcription
5
RNASeq
5
Regression
5
ChIPSeq
5
MethylationArray
4
CpGIsland
4
SingleCell
4
Bayesian
4
VariantDetection
4
MultipleComparison
4
CellBiology
4
SystemsBiology
4
Transcriptomics
4
Classification
4
MethylSeq
4
ExomeSeq
4
GeneRegulation
3
copy-number-variation
3
OneChannel
3
Network
3
StatisticalMethod
3
GeneticVariability
3
bioconductor-package
3
GenomeAnnotation
2
StructuralVariation
2
GenomeWideAssociation
2
FunctionalGenomics
2
Proteomics
2
FeatureExtraction
2
BiomedicalInformatics
2
Metabolomics
2
GeneTarget
2
mRNAMicroarray
2
GeneSetEnrichment
2
tumor-heterogeneity
2
bioconductor
2
bioinformatics
2
rstats
2
GraphAndNetwork
2
Epigenetics
2
genomics-visualization
2
BatchEffect
2
r-package
2
r
2
cell-free-dna
1
VariantAnnotation
1
Alignment
1
ATACSeq
1
SequenceMatching
1
Clustering.
1
FunctionalPrediction
1
LinkageDisequilibrium
1
Annotation
1
TargetedResequencing
1
WorkflowStep
1
Technology
1
ResearchField
1
Biological Question
1
AssayDomain
1
Survival
1
PrincipalComponent
1
Pathways
1
Lipidomics
1
GeneSignaling
1
GenePrediction
1
DimensionReduction
1
ChipOnChip
1
tumor-purity
1
tumor-mutational-burden
1
loh
1
copy-number
1
genomics
1
plotting-in-r
1
genome
1
data-visualization
1
hmm
1
genome-sequencing
1