Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "CopyNumberVariation" keyword
CINdex 1.30.0
Chromosome Instability Index3 versions - Latest release: 6 months ago - 11.5 thousand downloads total - 1 maintainer
Top 6.2% on bioconductor.org
3 versions - Latest release: 6 months ago - 50.4 thousand downloads total - 1 maintainer
cghMCR 1.60.0
Find chromosome regions showing common gains/losses3 versions - Latest release: 6 months ago - 50.4 thousand downloads total - 1 maintainer
tLOH 1.10.0
Assessment of evidence for LOH in spatial transcriptomics pre-processed data using Bayes factor c...3 versions - Latest release: 6 months ago - 2.68 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 7.1% on bioconductor.org
3 versions - Latest release: 6 months ago - 22.4 thousand downloads total - 87 stars on GitHub - 1 maintainer
TitanCNA 1.40.0
Subclonal copy number and LOH prediction from whole genome sequencing of tumours3 versions - Latest release: 6 months ago - 22.4 thousand downloads total - 87 stars on GitHub - 1 maintainer
CNVrd2 1.40.0
CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from...3 versions - Latest release: 6 months ago - 22.3 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 2.9% on bioconductor.org
3 versions - Latest release: 18 days ago - 8 dependent packages - 85.8 thousand downloads total - 287 stars on GitHub - 1 maintainer
karyoploteR 1.30.0
Plot customizable linear genomes displaying arbitrary data3 versions - Latest release: 18 days ago - 8 dependent packages - 85.8 thousand downloads total - 287 stars on GitHub - 1 maintainer
iCNV 1.22.0
Integrated Copy Number Variation detection3 versions - Latest release: 6 months ago - 7.74 thousand downloads total - 1 maintainer
BOBaFIT 1.6.0
Refitting diploid region profiles using a clustering procedure3 versions - Latest release: 6 months ago - 2.28 thousand downloads total - 0 stars on GitHub - 1 maintainer
conumee 1.36.0
Enhanced copy-number variation analysis using Illumina DNA methylation arrays3 versions - Latest release: 6 months ago - 23.8 thousand downloads total - 1 maintainer
sparsenetgls 1.20.0
Using Gaussian graphical structue learning estimation in generalized least squared regression for...3 versions - Latest release: 6 months ago - 5.7 thousand downloads total - 1 maintainer
Top 9.1% on bioconductor.org
3 versions - Latest release: 6 months ago - 28.4 thousand downloads total - 1 maintainer
KCsmart 2.60.0
Multi sample aCGH analysis package using kernel convolution3 versions - Latest release: 6 months ago - 28.4 thousand downloads total - 1 maintainer
VanillaICE 1.64.1
A Hidden Markov Model for high throughput genotyping arrays4 versions - Latest release: about 1 month ago - 2 dependent packages - 40 thousand downloads total - 1 maintainer
Top 9.6% on bioconductor.org
3 versions - Latest release: 6 months ago - 26.2 thousand downloads total - 1 maintainer
PREDA 1.48.0
Position Related Data Analysis3 versions - Latest release: 6 months ago - 26.2 thousand downloads total - 1 maintainer
MADSEQ 1.28.0
Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data3 versions - Latest release: 6 months ago - 9.99 thousand downloads total - 4 stars on GitHub - 1 maintainer
CNVfilteR 1.16.0
Identifies false positives of CNV calling tools by using SNV calls3 versions - Latest release: 6 months ago - 5.74 thousand downloads total - 3 stars on GitHub - 1 maintainer
CODEX 1.34.0
A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing3 versions - Latest release: 6 months ago - 1 dependent package - 23.4 thousand downloads total - 1 maintainer
panelcn.mops 1.24.0
CNV detection tool for targeted NGS panel data3 versions - Latest release: 6 months ago - 1 dependent package - 10.5 thousand downloads total - 1 maintainer
rcellminer 2.24.0
rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines3 versions - Latest release: 6 months ago - 15.7 thousand downloads total - 3 maintainers
iGC 1.32.0
An integrated analysis package of Gene expression and Copy number alteration3 versions - Latest release: 6 months ago - 11.3 thousand downloads total - 1 stars on GitHub - 1 maintainer
qsea 1.28.0
IP-seq data analysis and vizualization3 versions - Latest release: 6 months ago - 11.3 thousand downloads total - 1 maintainer
AMARETTO 1.18.0
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis an...3 versions - Latest release: 6 months ago - 7.55 thousand downloads total - 1 maintainer
Top 8.3% on bioconductor.org
3 versions - Latest release: 6 months ago - 30.2 thousand downloads total - 1 maintainer
MANOR 1.74.0
CGH Micro-Array NORmalization3 versions - Latest release: 6 months ago - 30.2 thousand downloads total - 1 maintainer
CNVPanelizer 1.34.0
Reliable CNV detection in targeted sequencing applications3 versions - Latest release: 6 months ago - 15.4 thousand downloads total - 1 maintainer
VegaMC 3.40.0
VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver ...3 versions - Latest release: 6 months ago - 21 thousand downloads total - 1 maintainer
Top 9.2% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 34.3 thousand downloads total - 1 maintainer
CGHregions 1.60.0
Dimension Reduction for Array CGH Data with Minimal Information Loss.3 versions - Latest release: 6 months ago - 1 dependent package - 34.3 thousand downloads total - 1 maintainer
regioneReloaded 1.4.0
RegioneReloaded: Multiple Association for Genomic Region Sets3 versions - Latest release: 6 months ago - 1.61 thousand downloads total - 5 stars on GitHub - 1 maintainer
BubbleTree 2.32.0
BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic m...3 versions - Latest release: 6 months ago - 16.2 thousand downloads total - 2 maintainers
CopyNumberPlots 1.18.0
Create Copy-Number Plots using karyoploteR functionality3 versions - Latest release: 6 months ago - 2 dependent packages - 9.48 thousand downloads total - 6 stars on GitHub - 1 maintainer
cn.farms 1.50.0
cn.FARMS - factor analysis for copy number estimation3 versions - Latest release: 6 months ago - 25.4 thousand downloads total - 1 maintainer
SCOPE 1.14.0
A normalization and copy number estimation method for single-cell DNA sequencing3 versions - Latest release: 6 months ago - 4.8 thousand downloads total - 1 maintainer
seqCNA 1.48.0 removed
Copy number analysis of high-throughput sequencing cancer data2 versions - Latest release: 6 months ago - 1 dependent package - 18.5 thousand downloads total - 1 maintainer
BiocOncoTK 1.22.2
Bioconductor components for general cancer genomics4 versions - Latest release: about 1 month ago - 9.97 thousand downloads total - 1 maintainer
biomvRCNS 1.42.2
Copy Number study and Segmentation for multivariate biological data4 versions - Latest release: 5 months ago - 21.4 thousand downloads total - 1 maintainer
Top 8.8% on bioconductor.org
3 versions - Latest release: 6 months ago - 26.9 thousand downloads total - 1 maintainer
SMAP 1.66.0
A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling3 versions - Latest release: 6 months ago - 26.9 thousand downloads total - 1 maintainer
snapCGH 1.72.0 removed
Segmentation, normalisation and processing of aCGH data2 versions - Latest release: 6 months ago - 2 dependent packages - 41.8 thousand downloads total - 1 maintainer
IntOMICS 1.2.0
Integrative analysis of multi-omics data to infer regulatory networks3 versions - Latest release: 6 months ago - 1.05 thousand downloads total - 0 stars on GitHub - 1 maintainer
CNAnorm 1.48.0
A normalization method for Copy Number Aberration in cancer samples3 versions - Latest release: 6 months ago - 26.9 thousand downloads total - 1 maintainer
GenomicOZone 1.16.0
Delineate outstanding genomic zones of differential gene activity3 versions - Latest release: 6 months ago - 5.21 thousand downloads total - 1 maintainer
GeoTcgaData 2.2.0
Processing Various Types of Data on GEO and TCGA3 versions - Latest release: 6 months ago - 1.61 thousand downloads total - 21 stars on GitHub - 1 maintainer
Top 8.9% on bioconductor.org
3 versions - Latest release: 6 months ago - 29.1 thousand downloads total - 1 maintainer
ITALICS 2.62.0
ITALICS3 versions - Latest release: 6 months ago - 29.1 thousand downloads total - 1 maintainer
GeneBreak 1.32.0
Gene Break Detection3 versions - Latest release: 6 months ago - 11.9 thousand downloads total - 2 stars on GitHub - 1 maintainer
MinimumDistance 1.46.0
A Package for De Novo CNV Detection in Case-Parent Trios3 versions - Latest release: 6 months ago - 22.6 thousand downloads total - 1 maintainer
CNViz 1.10.0
Copy Number Visualization3 versions - Latest release: 6 months ago - 2.93 thousand downloads total - 1 maintainer
Top 9.5% on bioconductor.org
3 versions - Latest release: 6 months ago - 37.6 thousand downloads total - 1 maintainer
beadarraySNP 1.68.0
Normalization and reporting of Illumina SNP bead arrays3 versions - Latest release: 6 months ago - 37.6 thousand downloads total - 1 maintainer
CNVRanger 1.18.1
Summarization and expression/phenotype association of CNV ranges4 versions - Latest release: 2 months ago - 8.7 thousand downloads total - 4 stars on GitHub - 1 maintainer
cfdnakit 1.2.0
Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA)3 versions - Latest release: 9 days ago - 991 downloads total - 6 stars on GitHub - 1 maintainer
Top 2.2% on bioconductor.org
3 versions - Latest release: 13 days ago - 13 dependent packages - 217 thousand downloads total - 1 maintainer
regioneR 1.36.0
Association analysis of genomic regions based on permutation tests3 versions - Latest release: 13 days ago - 13 dependent packages - 217 thousand downloads total - 1 maintainer
PureCN 2.10.0
Copy number calling and SNV classification using targeted short read sequencing4 versions - Latest release: 13 days ago - 25.8 thousand downloads total - 120 stars on GitHub - 1 maintainer
Top 5.0% on bioconductor.org
3 versions - Latest release: 12 days ago - 6 dependent packages - 71.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
CGHbase 1.64.0
CGHbase: Base functions and classes for arrayCGH data analysis.3 versions - Latest release: 12 days ago - 6 dependent packages - 71.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 5.4% on bioconductor.org
2 versions - Latest release: 6 months 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: 6 months ago - 3 dependent packages - 52.2 thousand downloads total - 1 maintainer
Top 3.8% on bioconductor.org
3 versions - Latest release: 13 days ago - 1 dependent package - 94.3 thousand downloads total - 1 maintainer
fastseg 1.50.0
fastseg - a fast segmentation algorithm3 versions - Latest release: 13 days ago - 1 dependent package - 94.3 thousand downloads total - 1 maintainer
Top 3.3% on bioconductor.org
3 versions - Latest release: 13 days ago - 4 dependent packages - 99.4 thousand downloads total - 1 maintainer
quantsmooth 1.70.0
Quantile smoothing and genomic visualization of array data3 versions - Latest release: 13 days ago - 4 dependent packages - 99.4 thousand downloads total - 1 maintainer
Top 4.3% on bioconductor.org
3 versions - Latest release: 13 days ago - 3 dependent packages - 69.9 thousand downloads total - 3 maintainers
crlmm 1.62.0
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumin...3 versions - Latest release: 13 days ago - 3 dependent packages - 69.9 thousand downloads total - 3 maintainers
Top 5.0% on bioconductor.org
3 versions - Latest release: 13 days ago - 1 dependent package - 64.3 thousand downloads total - 1 maintainer
HMMcopy 1.46.0
Copy number prediction with correction for GC and mappability bias for HTS data3 versions - Latest release: 13 days ago - 1 dependent package - 64.3 thousand downloads total - 1 maintainer
Top 4.2% on bioconductor.org
3 versions - Latest release: 13 days ago - 5 dependent packages - 83.4 thousand downloads total - 1 maintainer
GLAD 2.68.0
Gain and Loss Analysis of DNA3 versions - Latest release: 13 days ago - 5 dependent packages - 83.4 thousand downloads total - 1 maintainer
Top 6.0% on bioconductor.org
3 versions - Latest release: 13 days ago - 3 dependent packages - 54.7 thousand downloads total - 1 maintainer
cn.mops 1.50.0
cn.mops - Mixture of Poissons for CNV detection in NGS data3 versions - Latest release: 13 days ago - 3 dependent packages - 54.7 thousand downloads total - 1 maintainer
Top 5.5% on bioconductor.org
3 versions - Latest release: 13 days ago - 48.6 thousand downloads total - 1 maintainer
MEDIPS 1.56.0
DNA IP-seq data analysis3 versions - Latest release: 13 days ago - 48.6 thousand downloads total - 1 maintainer
Top 5.8% on bioconductor.org
3 versions - Latest release: 13 days ago - 1 dependent package - 55.9 thousand downloads total - 1 maintainer
CNTools 1.60.0
Convert segment data into a region by sample matrix to allow for other high level computational a...3 versions - Latest release: 13 days ago - 1 dependent package - 55.9 thousand downloads total - 1 maintainer
Top 5.4% on bioconductor.org
3 versions - Latest release: 20 days ago - 4 dependent packages - 48.1 thousand downloads total - 43 stars on GitHub - 1 maintainer
QDNAseq 1.40.0
Quantitative DNA Sequencing for Chromosomal Aberrations3 versions - Latest release: 20 days ago - 4 dependent packages - 48.1 thousand downloads total - 43 stars on GitHub - 1 maintainer
ACE 1.22.0
Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing3 versions - Latest release: 18 days ago - 8.72 thousand downloads total - 11 stars on GitHub - 1 maintainer
pgxRpi 1.0.0
R wrapper for Progenetix1 version - Latest release: 21 days ago - 197 downloads total - 2 stars on GitHub - 1 maintainer
gINTomics 1.0.0
Multi-Omics data integration1 version - Latest release: 21 days ago - 3 stars on GitHub - 1 maintainer
SARC 1.0.0
Statistical Analysis of Regions with CNVs1 version - Latest release: 7 months ago - 634 downloads total - 0 stars on GitHub - 1 maintainer
CNVMetrics 1.6.0
Copy Number Variant Metrics2 versions - Latest release: 6 months ago - 1.86 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 2.0% on bioconductor.org
2 versions - Latest release: 7 months ago - 29 dependent packages - 592 thousand downloads total - 1 maintainer
DNAcopy 1.76.0
DNA Copy Number Data Analysis2 versions - Latest release: 7 months ago - 29 dependent packages - 592 thousand downloads total - 1 maintainer
oncoscanR 1.4.0
Secondary analyses of CNV data (HRD and more)2 versions - Latest release: 6 months ago - 1.32 thousand downloads total - 2 stars on GitHub - 1 maintainer
partCNV 1.0.0
Infer locally aneuploid cells using single cell RNA-seq data1 version - Latest release: 7 months ago - 659 downloads total - 1 maintainer
rCGH 1.32.0
Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data2 versions - Latest release: 6 months ago - 1 dependent package - 15.6 thousand downloads total - 4 stars on GitHub - 1 maintainer
pathwayPCA 1.18.0
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection2 versions - Latest release: 6 months ago - 1 dependent package - 7.17 thousand downloads total - 11 stars on GitHub - 1 maintainer
MAGAR 1.10.0
MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation an...2 versions - Latest release: 6 months ago - 3.97 thousand downloads total - 0 stars on GitHub - 1 maintainer
AneuFinder 1.30.0
Analysis of Copy Number Variation in Single-Cell-Sequencing Data2 versions - Latest release: 6 months ago - 17 thousand downloads total - 15 stars on GitHub - 1 maintainer
Top 4.7% on bioconductor.org
3 versions - Latest release: 6 months ago - 77.8 thousand downloads total - 502 stars on GitHub - 1 maintainer
infercnv 1.18.1
Infer Copy Number Variation from Single-Cell RNA-Seq Data3 versions - Latest release: 6 months ago - 77.8 thousand downloads total - 502 stars on GitHub - 1 maintainer
Top 9.9% on bioconductor.org
2 versions - Latest release: 6 months ago - 25.7 thousand downloads total - 1 maintainer
mBPCR 1.56.0
Bayesian Piecewise Constant Regression for DNA copy number estimation2 versions - Latest release: 6 months ago - 25.7 thousand downloads total - 1 maintainer
aCGH 1.80.0
Classes and functions for Array Comparative Genomic Hybridization data2 versions - Latest release: 6 months ago - 5 dependent packages - 61.9 thousand downloads total - 1 maintainer
CopywriteR 2.32.0 removed
Copy number information from targeted sequencing using off-target reads1 version - Latest release: 7 months ago - 18.3 thousand downloads total - 28 stars on GitHub - 1 maintainer
Top 5.2% on bioconductor.org
1 version - Latest release: 7 months 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: 7 months ago - 1 dependent package - 57 thousand downloads total - 1 maintainer
Related Keywords
Software
76
Sequencing
31
Microarray
27
Visualization
21
Genetics
19
SNP
13
DNASeq
13
Preprocessing
13
Coverage
13
GenomicVariation
12
GeneExpression
12
DataImport
10
aCGH
9
Normalization
9
ImmunoOncology
9
QualityControl
9
DNAMethylation
8
WholeGenome
8
TwoChannel
6
DifferentialExpression
6
Regression
5
DifferentialMethylation
5
ChIPSeq
5
HiddenMarkovModel
5
Clustering
5
RNASeq
5
Transcription
5
Bayesian
4
CpGIsland
4
VariantDetection
4
CellBiology
4
MultipleComparison
4
MethylationArray
4
SystemsBiology
4
Transcriptomics
4
Classification
4
MethylSeq
4
ExomeSeq
4
SingleCell
4
Network
3
bioconductor-package
3
OneChannel
3
StatisticalMethod
3
GeneRegulation
3
GeneticVariability
3
copy-number-variation
3
GeneTarget
2
GenomeAnnotation
2
FunctionalGenomics
2
StructuralVariation
2
r-package
2
BatchEffect
2
GeneSetEnrichment
2
r
2
GenomeWideAssociation
2
mRNAMicroarray
2
Epigenetics
2
rstats
2
GraphAndNetwork
2
genomics-visualization
2
Metabolomics
2
bioinformatics
2
Proteomics
2
FeatureExtraction
2
bioconductor
2
tumor-heterogeneity
2
Lipidomics
1
Pathways
1
ATACSeq
1
GeneSignaling
1
GenePrediction
1
PrincipalComponent
1
Survival
1
VariantAnnotation
1
FunctionalPrediction
1
TargetedResequencing
1
cell-free-dna
1
copy-number
1
DimensionReduction
1
loh
1
tumor-mutational-burden
1
tumor-purity
1
Infrastructure
1
HapMap
1
Homo_sapiens
1
r-language
1
package
1
metrics
1
SequenceMatching
1
cnv
1
BiologicalQuestion
1
10x-genomics
1
genome-sequencing
1
hmm
1
Clustering.
1
LinkageDisequilibrium
1
data-visualization
1
genome
1
plotting-in-r
1
MassSpectrometry
1