Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "GenomicVariation" keyword
CINdex 1.30.0
Chromosome Instability Index3 versions - Latest release: 6 months ago - 11.5 thousand downloads total - 1 maintainer
cpvSNP 1.34.0
Gene set analysis methods for SNP association p-values that lie in genes in given gene sets3 versions - Latest release: 6 months ago - 13.3 thousand downloads total - 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
CrispRVariants 1.30.0
Tools for counting and visualising mutations in a target location3 versions - Latest release: 6 months ago - 17.1 thousand downloads total - 1 maintainer
geneAttribution 1.28.0
Identification of candidate genes associated with genetic variation3 versions - Latest release: 6 months ago - 10 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
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
RepViz 1.18.0
Replicate oriented Visualization of a genomic region3 versions - Latest release: 6 months ago - 6.28 thousand downloads total - 1 maintainer
myvariant 1.32.0
Accesses MyVariant.info variant query and annotation services3 versions - Latest release: 6 months ago - 15.5 thousand downloads total - 1 maintainer
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
decompTumor2Sig 2.18.0
Decomposition of individual tumors into mutational signatures by signature refitting3 versions - Latest release: 6 months ago - 1 dependent package - 8.89 thousand downloads total - 1 maintainer
TVTB 1.28.0
TVTB: The VCF Tool Box3 versions - Latest release: 6 months ago - 9.85 thousand downloads total - 2 stars on GitHub - 1 maintainer
scoreInvHap 1.24.0
Get inversion status in predefined regions3 versions - Latest release: 6 months ago - 7.93 thousand downloads total - 1 maintainer
kissDE 1.22.0
Retrieves Condition-Specific Variants in RNA-Seq Data3 versions - Latest release: 6 months ago - 8.07 thousand downloads total - 3 stars on GitHub - 1 maintainer
YAPSA 1.28.0
Yet Another Package for Signature Analysis3 versions - Latest release: 6 months ago - 16.5 thousand downloads total - 1 maintainer
RareVariantVis 2.30.0
A suite for analysis of rare genomic variants in whole genome sequencing data3 versions - Latest release: 6 months ago - 12.1 thousand downloads total - 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
semisup 1.26.0
Semi-Supervised Mixture Model3 versions - Latest release: 6 months ago - 7.99 thousand downloads total - 1 stars on GitHub - 1 maintainer
gmoviz 1.14.0
Seamless visualization of complex genomic variations in GMOs and edited cell lines3 versions - Latest release: 6 months ago - 4.38 thousand downloads total - 1 maintainer
ipdDb 1.20.0
IPD IMGT/HLA and IPD KIR database for Homo sapiens3 versions - Latest release: 6 months ago - 6.95 thousand downloads total - 0 stars on GitHub - 1 maintainer
COCOA 2.16.0
Coordinate Covariation Analysis3 versions - Latest release: 6 months ago - 7.09 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
branchpointer 1.28.0
Prediction of intronic splicing branchpoints3 versions - Latest release: 6 months ago - 10.5 thousand downloads total - 1 maintainer
signeR 2.6.0
Empirical Bayesian approach to mutational signature discovery3 versions - Latest release: 7 days ago - 14.2 thousand downloads total - 13 stars on GitHub - 1 maintainer
Top 3.3% on bioconductor.org
3 versions - Latest release: 13 days ago - 5 dependent packages - 122 thousand downloads total - 3 maintainers
missMethyl 1.38.0
Analysing Illumina HumanMethylation BeadChip Data3 versions - Latest release: 13 days ago - 5 dependent packages - 122 thousand downloads total - 3 maintainers
transmogR 1.0.0
Modify a set of reference sequences using a set of variants2 versions - Latest release: 19 days ago - 245 downloads total - 0 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
MungeSumstats 1.12.0
Standardise summary statistics from GWAS4 versions - Latest release: 20 days ago - 23 thousand downloads total - 64 stars on GitHub - 1 maintainer
RIVER 1.26.0
R package for RIVER (RNA-Informed Variant Effect on Regulation)2 versions - Latest release: 6 months ago - 8.53 thousand downloads total - 10 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
tadar 1.0.0
Transcriptome Analysis of Differential Allelic Representation1 version - Latest release: 7 months ago - 652 downloads total - 0 stars on GitHub - 1 maintainer
SomaticSignatures 2.38.0
Somatic Signatures2 versions - Latest release: 6 months ago - 1 dependent package - 42.8 thousand downloads total - 21 stars on GitHub - 1 maintainer
MouseFM 1.12.0
In-silico methods for genetic finemapping in inbred mice2 versions - Latest release: 6 months ago - 4.98 thousand downloads total - 0 stars on GitHub - 1 maintainer
seqCAT 1.24.0
High Throughput Sequencing Cell Authentication Toolkit2 versions - Latest release: 6 months ago - 8.41 thousand downloads total - 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
GeneAccord 1.18.0 removed
Detection of clonally exclusive gene or pathway pairs in a cohort of cancer patients1 version - Latest release: 7 months ago - 4.41 thousand downloads total - 2 stars on GitHub - 1 maintainer
Related Keywords
Software
38
Sequencing
20
Genetics
16
CopyNumberVariation
12
SNP
10
Visualization
8
SomaticMutation
7
Coverage
7
VariantAnnotation
7
StatisticalMethod
7
DNASeq
6
SystemsBiology
6
GeneticVariability
6
WholeGenome
6
FunctionalGenomics
6
GeneExpression
5
MultipleComparison
5
BiomedicalInformatics
5
Transcriptomics
5
Clustering
5
RNASeq
4
ImmunoOncology
4
VariantDetection
4
DifferentialExpression
4
GenomeWideAssociation
4
Microarray
4
GeneRegulation
3
Regression
3
Transcription
3
CellBiology
3
DNAMethylation
3
GeneSetEnrichment
3
Pathways
3
HiddenMarkovModel
3
DataRepresentation
3
GenePrediction
3
Bayesian
3
PatternLogic
2
Normalization
2
DifferentialMethylation
2
MathematicalBiology
2
FunctionalPrediction
2
ChIPSeq
2
StructuralVariation
2
ATACSeq
2
Classification
2
Epigenetics
2
GenomeAnnotation
2
GeneTarget
2
MethylationArray
2
PrincipalComponent
2
bioconductor-package
2
TranscriptomeVariant
2
FeatureExtraction
2
bioinformatics
2
qtl
2
Annotation
2
WorkflowStep
2
SequenceMatching
2
DataImport
2
Alignment
2
BiologicalQuestion
2
SingleCell
2
functional-variants
1
functionalgenomics
1
functionalprediction
1
generegulation
1
genetics
1
DimensionReduction
1
variant
1
transcriptomics
1
geneticvariability
1
transcriptomevariant
1
genomicvariation
1
snp
1
systemsbiology
1
transcription
1
GeneSignaling
1
Lipidomics
1
Metabolomics
1
Proteomics
1
Survival
1
finemap
1
gene-candidates
1
inbred-mice
1
inbred-strains
1
mouse
1
qtl-mapping
1
cancer
1
clonal
1
cooccurrence
1
exclusivity
1
mutual
1
aCGH
1
AnnotationHubSoftware
1
ExomeSeq
1
10x-genomics
1
copy-number-variation
1
genome-sequencing
1
hmm
1