bioconductor.org "CopyNumberVariation" keyword
rcellminer 2.32.0
rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines7 versions - Latest release: 4 months ago - 24.9 thousand downloads total - 3 maintainers
conumee 1.44.0
Enhanced copy-number variation analysis using Illumina DNA methylation arrays6 versions - Latest release: 4 months ago - 37.9 thousand downloads total - 1 maintainer
tLOH 1.18.0
Assessment of evidence for LOH in spatial transcriptomics pre-processed data using Bayes factor c...6 versions - Latest release: 4 months ago - 8.63 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 4.7% on bioconductor.org
7 versions - Latest release: 4 months ago - 167 thousand downloads total - 646 stars on GitHub - 1 maintainer
infercnv 1.26.0
Infer Copy Number Variation from Single-Cell RNA-Seq Data7 versions - Latest release: 4 months ago - 167 thousand downloads total - 646 stars on GitHub - 1 maintainer
Top 4.2% on bioconductor.org
6 versions - Latest release: 4 months ago - 5 dependent packages - 101 thousand downloads total - 1 maintainer
GLAD 2.74.0
Gain and Loss Analysis of DNA6 versions - Latest release: 4 months ago - 5 dependent packages - 101 thousand downloads total - 1 maintainer
ELViS 1.2.0
An R Package for Estimating Copy Number Levels of Viral Genome Segments Using Base-Resolution Rea...2 versions - Latest release: 4 months ago - 2.85 thousand downloads total - 0 stars on GitHub - 1 maintainer
CNVfilteR 1.24.0
Identifies false positives of CNV calling tools by using SNV calls7 versions - Latest release: 4 months ago - 11.9 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 6.0% on bioconductor.org
6 versions - Latest release: 4 months ago - 3 dependent packages - 70 thousand downloads total - 1 maintainer
cn.mops 1.56.0
cn.mops - Mixture of Poissons for CNV detection in NGS data6 versions - Latest release: 4 months ago - 3 dependent packages - 70 thousand downloads total - 1 maintainer
ACE 1.28.0
Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing6 versions - Latest release: 4 months ago - 18.3 thousand downloads total - 18 stars on GitHub - 1 maintainer
MAGAR 1.18.0
MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation an...6 versions - Latest release: 4 months ago - 10.7 thousand downloads total - 0 stars on GitHub - 1 maintainer
gINTomics 1.6.0
Multi-Omics data integration6 versions - Latest release: about 2 months ago - 3.93 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 9.1% on bioconductor.org
6 versions - Latest release: 4 months ago - 37.4 thousand downloads total - 1 maintainer
KCsmart 2.68.0
Multi sample aCGH analysis package using kernel convolution6 versions - Latest release: 4 months ago - 37.4 thousand downloads total - 1 maintainer
SARC 1.7.1
Statistical Analysis of Regions with CNVs5 versions - Latest release: 4 months ago - 5.26 thousand downloads total - 0 stars on GitHub - 1 maintainer
biomvRCNS 1.50.0
Copy Number study and Segmentation for multivariate biological data7 versions - Latest release: 4 months ago - 30.9 thousand downloads total - 1 maintainer
Top 9.6% on bioconductor.org
6 versions - Latest release: 4 months ago - 35.5 thousand downloads total - 1 maintainer
PREDA 1.56.0
Position Related Data Analysis6 versions - Latest release: 4 months ago - 35.5 thousand downloads total - 1 maintainer
BOBaFIT 1.14.0
Refitting diploid region profiles using a clustering procedure6 versions - Latest release: 4 months ago - 8.32 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 9.9% on bioconductor.org
6 versions - Latest release: 4 months ago - 34.7 thousand downloads total - 1 maintainer
mBPCR 1.64.0
Bayesian Piecewise Constant Regression for DNA copy number estimation6 versions - Latest release: 4 months ago - 34.7 thousand downloads total - 1 maintainer
dmGsea 1.0.2
Efficient Gene Set Enrichment Analysis for DNA Methylation Data3 versions - Latest release: about 2 months ago - 2.25 thousand downloads total - 1 maintainer
CNVrd2 1.48.0
CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from...6 versions - Latest release: 4 months ago - 30.3 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 2.9% on bioconductor.org
7 versions - Latest release: 4 months ago - 8 dependent packages - 141 thousand downloads total - 344 stars on GitHub - 1 maintainer
karyoploteR 1.36.0
Plot customizable linear genomes displaying arbitrary data7 versions - Latest release: 4 months ago - 8 dependent packages - 141 thousand downloads total - 344 stars on GitHub - 1 maintainer
VanillaICE 1.72.0
A Hidden Markov Model for high throughput genotyping arrays8 versions - Latest release: 4 months ago - 2 dependent packages - 53.3 thousand downloads total - 1 maintainer
GeoTcgaData 2.10.0
Processing Various Types of Data on GEO and TCGA6 versions - Latest release: 4 months ago - 8.81 thousand downloads total - 28 stars on GitHub - 1 maintainer
GeneBreak 1.40.0
Gene Break Detection6 versions - Latest release: 4 months ago - 19.6 thousand downloads total - 2 stars on GitHub - 1 maintainer
BubbleTree 2.39.0
BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic m...6 versions - Latest release: 4 months ago - 23.6 thousand downloads total - 2 maintainers
panelcn.mops 1.32.0
CNV detection tool for targeted NGS panel data6 versions - Latest release: 4 months ago - 1 dependent package - 19.8 thousand downloads total - 1 maintainer
partCNV 1.8.0
Infer locally aneuploid cells using single cell RNA-seq data5 versions - Latest release: 4 months ago - 5.83 thousand downloads total - 1 maintainer
CNViz 1.18.0
Copy Number Visualization6 versions - Latest release: 4 months ago - 8.04 thousand downloads total - 1 maintainer
CNAnorm 1.56.0
A normalization method for Copy Number Aberration in cancer samples6 versions - Latest release: 4 months ago - 34.8 thousand downloads total - 1 maintainer
GenomicOZone 1.24.0
Delineate outstanding genomic zones of differential gene activity6 versions - Latest release: 4 months ago - 11.6 thousand downloads total - 1 maintainer
Top 8.9% on bioconductor.org
6 versions - Latest release: 4 months ago - 39.1 thousand downloads total - 1 maintainer
ITALICS 2.70.0
ITALICS6 versions - Latest release: 4 months ago - 39.1 thousand downloads total - 1 maintainer
CINdex 1.38.0
Chromosome Instability Index7 versions - Latest release: about 2 months ago - 18.2 thousand downloads total - 1 maintainer
cn.farms 1.58.0
cn.FARMS - factor analysis for copy number estimation7 versions - Latest release: 4 months ago - 45.1 thousand downloads total - 1 maintainer
CNVPanelizer 1.42.0
Reliable CNV detection in targeted sequencing applications6 versions - Latest release: 4 months ago - 23.5 thousand downloads total - 1 maintainer
Top 6.2% on bioconductor.org
6 versions - Latest release: 4 months ago - 60.4 thousand downloads total - 1 maintainer
cghMCR 1.68.0
Find chromosome regions showing common gains/losses6 versions - Latest release: 4 months ago - 60.4 thousand downloads total - 1 maintainer
aCGH 1.88.0
Classes and functions for Array Comparative Genomic Hybridization data6 versions - Latest release: 4 months ago - 5 dependent packages - 80.1 thousand downloads total - 1 maintainer
MinimumDistance 1.54.0
A Package for De Novo CNV Detection in Case-Parent Trios7 versions - Latest release: 4 months ago - 31.9 thousand downloads total - 1 maintainer
CopyNumberPlots 1.26.0
Create Copy-Number Plots using karyoploteR functionality7 versions - Latest release: 4 months ago - 2 dependent packages - 16.5 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 2.0% on bioconductor.org
6 versions - Latest release: 4 months ago - 29 dependent packages - 782 thousand downloads total - 1 maintainer
DNAcopy 1.84.0
DNA Copy Number Data Analysis6 versions - Latest release: 4 months ago - 29 dependent packages - 782 thousand downloads total - 1 maintainer
AMARETTO 1.26.0
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis an...6 versions - Latest release: 4 months ago - 17.2 thousand downloads total - 1 maintainer
Top 5.0% on bioconductor.org
6 versions - Latest release: 4 months ago - 6 dependent packages - 104 thousand downloads total - 0 stars on GitHub - 1 maintainer
CGHbase 1.70.0
CGHbase: Base functions and classes for arrayCGH data analysis.6 versions - Latest release: 4 months ago - 6 dependent packages - 104 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 5.0% on bioconductor.org
6 versions - Latest release: 4 months ago - 1 dependent package - 82.8 thousand downloads total - 1 maintainer
HMMcopy 1.52.0
Copy number prediction with correction for GC and mappability bias for HTS data6 versions - Latest release: 4 months ago - 1 dependent package - 82.8 thousand downloads total - 1 maintainer
iCNV 1.30.0
Integrated Copy Number Variation detection6 versions - Latest release: 4 months ago - 14.5 thousand downloads total - 1 maintainer
Top 5.8% on bioconductor.org
6 versions - Latest release: 4 months ago - 1 dependent package - 66.1 thousand downloads total - 1 maintainer
CNTools 1.66.0
Convert segment data into a region by sample matrix to allow for other high level computational a...6 versions - Latest release: 4 months ago - 1 dependent package - 66.1 thousand downloads total - 1 maintainer
Top 9.2% on bioconductor.org
6 versions - Latest release: 4 months ago - 1 dependent package - 43.4 thousand downloads total - 1 maintainer
CGHregions 1.68.0
Dimension Reduction for Array CGH Data with Minimal Information Loss.6 versions - Latest release: 4 months ago - 1 dependent package - 43.4 thousand downloads total - 1 maintainer
CNVRanger 1.26.0
Summarization and expression/phenotype association of CNV ranges8 versions - Latest release: 4 months ago - 15.9 thousand downloads total - 4 stars on GitHub - 1 maintainer
CODEX 1.42.0
A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing6 versions - Latest release: 4 months ago - 1 dependent package - 33 thousand downloads total - 1 maintainer
Top 7.1% on bioconductor.org
6 versions - Latest release: 4 months ago - 29.4 thousand downloads total - 87 stars on GitHub - 1 maintainer
TitanCNA 1.48.0
Subclonal copy number and LOH prediction from whole genome sequencing of tumours6 versions - Latest release: 4 months ago - 29.4 thousand downloads total - 87 stars on GitHub - 1 maintainer
Top 3.3% on bioconductor.org
6 versions - Latest release: 4 months ago - 4 dependent packages - 142 thousand downloads total - 1 maintainer
quantsmooth 1.76.0
Quantile smoothing and genomic visualization of array data6 versions - Latest release: 4 months ago - 4 dependent packages - 142 thousand downloads total - 1 maintainer
VegaMC 3.48.0
VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver ...6 versions - Latest release: 4 months ago - 29.5 thousand downloads total - 1 maintainer
SCOPE 1.22.0
A normalization and copy number estimation method for single-cell DNA sequencing6 versions - Latest release: 4 months ago - 11.7 thousand downloads total - 1 maintainer
Top 5.5% on bioconductor.org
6 versions - Latest release: 4 months ago - 63 thousand downloads total - 1 maintainer
MEDIPS 1.62.0
DNA IP-seq data analysis6 versions - Latest release: 4 months ago - 63 thousand downloads total - 1 maintainer
Top 2.2% on bioconductor.org
7 versions - Latest release: 4 months ago - 13 dependent packages - 329 thousand downloads total - 1 maintainer
regioneR 1.42.0
Association analysis of genomic regions based on permutation tests7 versions - Latest release: 4 months ago - 13 dependent packages - 329 thousand downloads total - 1 maintainer
cfdnakit 1.8.0
Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA)6 versions - Latest release: 4 months ago - 6.48 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 4.3% on bioconductor.org
7 versions - Latest release: 4 months ago - 3 dependent packages - 86.1 thousand downloads total - 3 maintainers
crlmm 1.68.0
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumin...7 versions - Latest release: 4 months ago - 3 dependent packages - 86.1 thousand downloads total - 3 maintainers
pathwayPCA 1.26.0
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection6 versions - Latest release: 4 months ago - 1 dependent package - 15.2 thousand downloads total - 11 stars on GitHub - 1 maintainer
regioneReloaded 1.12.0
RegioneReloaded: Multiple Association for Genomic Region Sets6 versions - Latest release: 4 months ago - 7.04 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 5.4% on bioconductor.org
6 versions - Latest release: 4 months ago - 4 dependent packages - 78.2 thousand downloads total - 52 stars on GitHub - 1 maintainer
QDNAseq 1.46.0
Quantitative DNA Sequencing for Chromosomal Aberrations6 versions - Latest release: 4 months ago - 4 dependent packages - 78.2 thousand downloads total - 52 stars on GitHub - 1 maintainer
rCGH 1.40.0
Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data6 versions - Latest release: 4 months ago - 1 dependent package - 27.4 thousand downloads total - 4 stars on GitHub - 1 maintainer
PureCN 2.16.1
Copy number calling and SNV classification using targeted short read sequencing10 versions - Latest release: 24 days ago - 37.5 thousand downloads total - 144 stars on GitHub - 1 maintainer
Top 8.3% on bioconductor.org
6 versions - Latest release: 5 months ago - 40.1 thousand downloads total - 1 maintainer
MANOR 1.82.0
CGH Micro-Array NORmalization6 versions - Latest release: 5 months ago - 40.1 thousand downloads total - 1 maintainer
qsea 1.36.0
IP-seq data analysis and vizualization6 versions - Latest release: 4 months ago - 18.4 thousand downloads total - 1 maintainer
CNVMetrics 1.14.2
Copy Number Variant Metrics7 versions - Latest release: 2 months ago - 7.61 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 3.8% on bioconductor.org
6 versions - Latest release: 4 months ago - 1 dependent package - 151 thousand downloads total - 1 maintainer
fastseg 1.56.0
fastseg - a fast segmentation algorithm6 versions - Latest release: 4 months ago - 1 dependent package - 151 thousand downloads total - 1 maintainer
AneuFinder 1.35.0 removed
Analysis of Copy Number Variation in Single-Cell-Sequencing Data5 versions - Latest release: 11 months ago - 37.4 thousand downloads total - 18 stars on GitHub - 1 maintainer
sparsenetgls 1.28.0
Using Gaussian graphical structue learning estimation in generalized least squared regression for...6 versions - Latest release: 4 months ago - 11.3 thousand downloads total - 1 maintainer
pgxRpi 1.6.0
R wrapper for Progenetix13 versions - Latest release: 4 months ago - 5.67 thousand downloads total - 3 stars on GitHub - 1 maintainer
MADSEQ 1.36.0
Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data6 versions - Latest release: 4 months ago - 15.5 thousand downloads total - 4 stars on GitHub - 1 maintainer
iGC 1.36.0
An integrated analysis package of Gene expression and Copy number alteration4 versions - Latest release: over 1 year ago - 13.3 thousand downloads total - 1 stars on GitHub - 1 maintainer
oncoscanR 1.6.0
Secondary analyses of CNV data (HRD and more)3 versions - Latest release: almost 2 years ago - 3.04 thousand downloads total - 3 stars on GitHub - 1 maintainer
CopywriteR 2.32.0 removed
Copy number information from targeted sequencing using off-target reads1 version - Latest release: over 2 years ago - 18.3 thousand downloads total - 32 stars on GitHub - 1 maintainer
IntOMICS 1.4.0 removed
Integrative analysis of multi-omics data to infer regulatory networks3 versions - Latest release: almost 2 years 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: over 1 year ago - 13.4 thousand downloads total - 1 maintainer
Top 9.5% on bioconductor.org
3 versions - Latest release: almost 2 years ago - 38.5 thousand downloads total - 1 maintainer
beadarraySNP 1.70.0 removed
Normalization and reporting of Illumina SNP bead arrays3 versions - Latest release: almost 2 years ago - 38.5 thousand downloads total - 1 maintainer
Top 8.8% on bioconductor.org
3 versions - Latest release: almost 2 years 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: almost 2 years 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 2 years 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 2 years ago - 2 dependent packages - 41.8 thousand downloads total - 1 maintainer
Top 5.4% on bioconductor.org
2 versions - Latest release: over 2 years 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 2 years ago - 3 dependent packages - 52.2 thousand downloads total - 1 maintainer
Top 5.2% on bioconductor.org
1 version - Latest release: over 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: over 2 years ago - 1 dependent package - 57 thousand downloads total - 1 maintainer
Related Keywords
Software
78
Sequencing
33
Microarray
27
Visualization
22
Genetics
19
Coverage
15
GenomicVariation
14
DNASeq
13
GeneExpression
13
SNP
13
Preprocessing
13
DataImport
10
Normalization
10
QualityControl
9
DNAMethylation
9
ImmunoOncology
9
aCGH
9
WholeGenome
8
Clustering
6
TwoChannel
6
DifferentialExpression
6
ChIPSeq
5
RNASeq
5
Regression
5
DifferentialMethylation
5
HiddenMarkovModel
5
Transcription
5
ExomeSeq
4
VariantDetection
4
SingleCell
4
Bayesian
4
Transcriptomics
4
MethylationArray
4
CellBiology
4
SystemsBiology
4
MultipleComparison
4
Classification
4
MethylSeq
4
CpGIsland
4
OneChannel
3
Network
3
GeneSetEnrichment
3
Proteomics
3
GeneticVariability
3
copy-number-variation
3
bioconductor-package
3
StatisticalMethod
3
GeneRegulation
3
bioconductor
2
bioinformatics
2
Metabolomics
2
genomics-visualization
2
rstats
2
GenomeWideAssociation
2
Pathways
2
GeneTarget
2
mRNAMicroarray
2
GraphAndNetwork
2
Epigenetics
2
BatchEffect
2
FunctionalGenomics
2
r
2
BiomedicalInformatics
2
StructuralVariation
2
r-package
2
tumor-heterogeneity
2
FeatureExtraction
2
GenomeAnnotation
2
cell-free-dna
1
copy-number
1
TargetedResequencing
1
VariantAnnotation
1
Survival
1
PrincipalComponent
1
Lipidomics
1
GeneSignaling
1
GenePrediction
1
DimensionReduction
1
WorkflowStep
1
Technology
1
ResearchField
1
Biological Question
1
AssayDomain
1
SomaticMutation
1
MassSpectrometry
1
r-language
1
package
1
metrics
1
cnv
1
BiologicalQuestion
1
ChipOnChip
1
tumor-purity
1
tumor-mutational-burden
1
loh
1
CellBasedAssays
1
Cheminformatics
1
Pharmacogenetics
1
Pharmacogenomics
1
miRNA
1
HapMap
1