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bioconductor.org "SNP" keyword

View the packages on the bioconductor.org package registry that are tagged with the "SNP" keyword.

Top 9.0% on bioconductor.org
RLMM 1.70.0
A Genotype Calling Algorithm for Affymetrix SNP Arrays
5 versions - Latest release: 2 months ago - 32 thousand downloads total - 1 maintainer
Top 0.8% on bioconductor.org
BSgenome 1.76.0
Software infrastructure for efficient representation of full genomes and their SNPs
7 versions - Latest release: 3 months ago - 129 dependent packages - 2.39 million downloads total - 1 maintainer
Top 5.9% on bioconductor.org
systemPipeR 2.14.2
systemPipeR: Workflow Environment for Data Analysis and Report Generation
6 versions - Latest release: 29 days ago - 3 dependent packages - 239 thousand downloads total - 53 stars on GitHub - 1 maintainer
Top 1.8% on bioconductor.org
Rsubread 2.22.1
Mapping, quantification and variant analysis of sequencing data
7 versions - Latest release: 3 months ago - 14 dependent packages - 363 thousand downloads total - 2 maintainers
Top 0.6% on bioconductor.org
GenomicAlignments 1.44.0
Representation and manipulation of short genomic alignments
7 versions - Latest release: 3 months ago - 132 dependent packages - 4.18 million downloads total - 1 maintainer
Top 0.9% on bioconductor.org
VariantAnnotation 1.54.1
Annotation of Genetic Variants
7 versions - Latest release: 3 months ago - 93 dependent packages - 1.81 million downloads total - 1 maintainer
CCAFE 1.0.0
Case Control Allele Frequency Estimation
1 version - Latest release: 3 months ago - 1.35 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
snpStats 1.58.0
SnpMatrix and XSnpMatrix classes and methods
5 versions - Latest release: 2 months ago - 15 dependent packages - 443 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
Top 4.1% on bioconductor.org
GWASTools 1.54.0
Tools for Genome Wide Association Studies
5 versions - Latest release: 3 months ago - 4 dependent packages - 114 thousand downloads total - 18 stars on GitHub - 1 maintainer
Top 6.9% on bioconductor.org
lfa 2.8.0
Logistic Factor Analysis for Categorical Data
5 versions - Latest release: 2 months ago - 1 dependent package - 49.6 thousand downloads total - 16 stars on GitHub - 1 maintainer
Top 4.6% on bioconductor.org
SeqVarTools 1.46.0
Tools for variant data
5 versions - Latest release: 3 months ago - 1 dependent package - 72 thousand downloads total - 3 stars on GitHub - 1 maintainer
RIVER 1.32.0
R package for RIVER (RNA-Informed Variant Effect on Regulation)
5 versions - Latest release: 3 months ago - 13.5 thousand downloads total - 10 stars on GitHub - 1 maintainer
scQTLtools 1.0.3
An R package for single-cell eQTL analysis and visualization
3 versions - Latest release: about 1 month ago - 1.44 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 3.2% on bioconductor.org
oligo 1.72.0
Preprocessing tools for oligonucleotide arrays
7 versions - Latest release: 2 months ago - 11 dependent packages - 437 thousand downloads total - 3 stars on GitHub - 1 maintainer
Qtlizer 1.22.0
Comprehensive QTL annotation of GWAS results
6 versions - Latest release: 3 months ago - 10.5 thousand downloads total - 3 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
tadar 1.6.0
Transcriptome Analysis of Differential Allelic Representation
5 versions - Latest release: 3 months ago - 4.24 thousand downloads total - 1 stars on GitHub - 1 maintainer
epistasisGA 1.10.0
An R package to identify multi-snp effects in nuclear family studies using the GADGETS method
5 versions - Latest release: 3 months ago - 5 thousand downloads total - 1 stars on GitHub - 1 maintainer
GeneGeneInteR 1.33.0
Tools for Testing Gene-Gene Interaction at the Gene Level
5 versions - Latest release: 3 months ago - 14.5 thousand downloads total - 1 maintainer
MungeSumstats 1.16.0
Standardise summary statistics from GWAS
7 versions - Latest release: 2 months ago - 41.6 thousand downloads total - 83 stars on GitHub - 1 maintainer
QTLExperiment 2.0.1
S4 classes for QTL summary statistics and metadata
4 versions - Latest release: 3 months ago - 1 dependent package - 4.15 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 7.6% on bioconductor.org
DRIMSeq 1.36.0
Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
5 versions - Latest release: 3 months ago - 1 dependent package - 47.9 thousand downloads total - 1 maintainer
MouseFM 1.18.0
In-silico methods for genetic finemapping in inbred mice
6 versions - Latest release: 3 months ago - 9.91 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 3.8% on bioconductor.org
siggenes 1.82.0
Multiple Testing using SAM and Efron's Empirical Bayes Approaches
5 versions - Latest release: 3 months ago - 6 dependent packages - 497 thousand downloads total - 1 maintainer
IMAS 1.32.0
Integrative analysis of Multi-omics data for Alternative Splicing
5 versions - Latest release: 3 months ago - 13.9 thousand downloads total - 1 maintainer
multistateQTL 2.0.0
Toolkit for the analysis of multi-state QTL data
4 versions - Latest release: 3 months ago - 3.22 thousand downloads total - 1 stars on GitHub - 1 maintainer
SigsPack 1.22.0
Mutational Signature Estimation for Single Samples
5 versions - Latest release: 3 months ago - 8.55 thousand downloads total - 2 stars on GitHub - 1 maintainer
hapFabia 1.50.0
hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rar...
5 versions - Latest release: 3 months ago - 26.7 thousand downloads total - 1 maintainer
G4SNVHunter 1.0.0
Evaluating SNV-Induced Disruption of G-Quadruplex Structures
1 version - Latest release: 3 months ago - 1.68 thousand downloads total - 0 stars on GitHub - 1 maintainer
gwasurvivr 1.26.0
gwasurvivr: an R package for genome wide survival analysis
5 versions - Latest release: 3 months ago - 14.4 thousand downloads total - 12 stars on GitHub - 1 maintainer
REBET 1.26.0
The subREgion-based BurdEn Test (REBET)
5 versions - Latest release: 3 months ago - 9.12 thousand downloads total - 1 maintainer
cageminer 1.14.0
Candidate Gene Miner
5 versions - Latest release: 3 months ago - 6.48 thousand downloads total - 1 stars on GitHub - 1 maintainer
AlphaMissenseR 1.4.0
Accessing AlphaMissense Data Resources in R
5 versions - Latest release: 3 months ago - 3.74 thousand downloads total - 8 stars on GitHub - 1 maintainer
Top 5.2% on bioconductor.org
GENESIS 2.38.0
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzi...
5 versions - Latest release: 3 months ago - 1 dependent package - 66.5 thousand downloads total - 38 stars on GitHub - 1 maintainer
OPWeight 1.30.0
Optimal p-value weighting with independent information
5 versions - Latest release: 3 months ago - 20.4 thousand downloads total - 2 stars on GitHub - 1 maintainer
GGPA 1.20.0
graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architec...
5 versions - Latest release: 3 months ago - 7.79 thousand downloads total - 1 stars on GitHub - 1 maintainer
gcatest 2.8.0
Genotype Conditional Association TEST
5 versions - Latest release: 2 months ago - 15 thousand downloads total - 5 stars on GitHub - 1 maintainer
metaCCA 1.36.0
Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Cano...
5 versions - Latest release: 3 months ago - 16.8 thousand downloads total - 1 maintainer
mbQTL 1.8.0
mbQTL: A package for SNP-Taxa mGWAS analysis
5 versions - Latest release: 3 months ago - 4.37 thousand downloads total - 1 maintainer
Top 4.3% on bioconductor.org
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
Top 4.6% on bioconductor.org
qpgraph 2.42.0
Estimation of Genetic and Molecular Regulatory Networks from High-Throughput Genomics Data
5 versions - Latest release: 3 months ago - 1 dependent package - 61.3 thousand downloads total - 3 stars on GitHub - 1 maintainer
trigger 1.53.0
Transcriptional Regulatory Inference from Genetics of Gene ExpRession
5 versions - Latest release: 3 months ago - 26.9 thousand downloads total - 1 maintainer
INPower 1.44.0
An R package for computing the number of susceptibility SNPs
5 versions - Latest release: 3 months ago - 19.3 thousand downloads total - 1 maintainer
trio 3.46.0
Testing of SNPs and SNP Interactions in Case-Parent Trio Studies
5 versions - Latest release: 3 months ago - 29 thousand downloads total - 1 maintainer
CNVRanger 1.24.2
Summarization and expression/phenotype association of CNV ranges
7 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 Trios
6 versions - Latest release: about 2 months ago - 27.9 thousand downloads total - 1 maintainer
Top 4.6% on bioconductor.org
sangerseqR 1.44.0
Tools for Sanger Sequencing Data in R
5 versions - Latest release: 3 months ago - 3 dependent packages - 81.5 thousand downloads total - 1 maintainer
IVAS 2.28.0
Identification of genetic Variants affecting Alternative Splicing
5 versions - Latest release: 3 months ago - 1 dependent package - 18.6 thousand downloads total - 1 maintainer
iBMQ 1.48.0
integrated Bayesian Modeling of eQTL data
5 versions - Latest release: 3 months ago - 20.4 thousand downloads total - 1 maintainer
iCNV 1.28.0
Integrated Copy Number Variation detection
5 versions - Latest release: 3 months ago - 12 thousand downloads total - 1 maintainer
BBCAnalyzer 1.38.0
BBCAnalyzer: an R/Bioconductor package for visualizing base counts
5 versions - Latest release: 3 months ago - 18.5 thousand downloads total - 1 maintainer
Top 9.4% on bioconductor.org
GeneRegionScan 1.64.0
GeneRegionScan
5 versions - Latest release: 3 months ago - 34 thousand downloads total - 1 maintainer
Top 8.5% on bioconductor.org
deepSNV 1.54.0
Detection of subclonal SNVs in deep sequencing data.
5 versions - Latest release: 3 months ago - 2 dependent packages - 42 thousand downloads total - 1 maintainer
Top 9.9% on bioconductor.org
MassArray 1.60.0
Analytical Tools for MassArray Data
5 versions - Latest release: 3 months ago - 30.1 thousand downloads total - 1 maintainer
hierinf 1.26.0
Hierarchical Inference
5 versions - Latest release: 3 months ago - 8.5 thousand downloads total - 1 maintainer
ProteoDisco 1.14.0
Generation of customized protein variant databases from genomic variants, splice-junctions and ma...
5 versions - Latest release: 3 months ago - 5.89 thousand downloads total - 5 stars on GitHub - 1 maintainer
scoreInvHap 1.30.0
Get inversion status in predefined regions
5 versions - Latest release: 3 months ago - 12.2 thousand downloads total - 1 maintainer
iASeq 1.52.0
iASeq: integrating multiple sequencing datasets for detecting allele-specific events
5 versions - Latest release: 3 months ago - 24.9 thousand downloads total - 1 maintainer
GEM 1.34.0
GEM: fast association study for the interplay of Gene, Environment and Methylation
5 versions - Latest release: 3 months ago - 13.7 thousand downloads total - 1 maintainer
SNPediaR 1.34.0
Query data from SNPedia
5 versions - Latest release: 3 months ago - 13.1 thousand downloads total - 10 stars on GitHub - 1 maintainer
sitePath 1.24.0
Phylogeny-based sequence clustering with site polymorphism
5 versions - Latest release: 3 months ago - 8.99 thousand downloads total - 9 stars on GitHub - 1 maintainer
katdetectr 1.10.0
Detection, Characterization and Visualization of Kataegis in Sequencing Data
5 versions - Latest release: 3 months ago - 5.26 thousand downloads total - 1 maintainer
GeoTcgaData 2.8.0
Processing Various Types of Data on GEO and TCGA
5 versions - Latest release: 3 months ago - 6.23 thousand downloads total - 26 stars on GitHub - 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
customProDB 1.48.0
Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics ...
6 versions - Latest release: 3 months ago - 30.7 thousand downloads total - 1 maintainer
appreci8R 1.26.0
appreci8R: an R/Bioconductor package for filtering SNVs and short indels with high sensitivity an...
6 versions - Latest release: 3 months ago - 11.6 thousand downloads total - 1 maintainer
decompTumor2Sig 2.24.0
Decomposition of individual tumors into mutational signatures by signature refitting
5 versions - Latest release: 3 months ago - 1 dependent package - 14.5 thousand downloads total - 1 maintainer
Top 7.5% on bioconductor.org
chopsticks 1.74.0
The 'snp.matrix' and 'X.snp.matrix' Classes
5 versions - Latest release: 3 months ago - 45.3 thousand downloads total - 1 maintainer
SICtools 1.38.0
Find SNV/Indel differences between two bam files with near relationship
5 versions - Latest release: 3 months ago - 14.7 thousand downloads total - 1 maintainer
Top 9.9% on bioconductor.org
mBPCR 1.62.0
Bayesian Piecewise Constant Regression for DNA copy number estimation
5 versions - Latest release: 3 months ago - 30.9 thousand downloads total - 1 maintainer
ISoLDE 1.36.0
Integrative Statistics of alleLe Dependent Expression
5 versions - Latest release: 3 months ago - 12.5 thousand downloads total - 1 maintainer
BG2 1.8.0
Performs Bayesian GWAS analysis for non-Gaussian data using BG2
5 versions - Latest release: 3 months ago - 4.45 thousand downloads total - 1 maintainer
hierGWAS 1.38.0
Asessing statistical significance in predictive GWA studies
5 versions - Latest release: 3 months ago - 15.8 thousand downloads total - 1 maintainer
GIGSEA 1.26.0
Genotype Imputed Gene Set Enrichment Analysis
5 versions - Latest release: 3 months ago - 9.19 thousand downloads total - 1 maintainer
geneAttribution 1.34.0
Identification of candidate genes associated with genetic variation
5 versions - Latest release: 3 months ago - 14.3 thousand downloads total - 1 maintainer
Top 7.7% on bioconductor.org
CGEN 3.44.0
An R package for analysis of case-control studies in genetic epidemiology
5 versions - Latest release: 3 months ago - 41.5 thousand downloads total - 1 maintainer
GWAS.BAYES 1.18.0
Bayesian analysis of Gaussian GWAS data
5 versions - Latest release: 3 months ago - 7.36 thousand downloads total - 1 maintainer
Top 6.2% on bioconductor.org
logicFS 2.28.0
Identification of SNP Interactions
5 versions - Latest release: 3 months ago - 1 dependent package - 46 thousand downloads total - 1 maintainer
ASAFE 1.34.0
Ancestry Specific Allele Frequency Estimation
5 versions - Latest release: 3 months ago - 15.1 thousand downloads total - 1 maintainer
ASSET 2.26.0
An R package for subset-based association analysis of heterogeneous traits and subtypes
5 versions - Latest release: 3 months ago - 1 dependent package - 28.2 thousand downloads total - 1 maintainer
martini 1.28.0
GWAS Incorporating Networks
5 versions - Latest release: 3 months ago - 11.9 thousand downloads total - 4 stars on GitHub - 1 maintainer
VariantFiltering 1.44.0
Filtering of coding and non-coding genetic variants
5 versions - Latest release: 2 months ago - 30 thousand downloads total - 4 stars on GitHub - 1 maintainer
GPA 1.20.0
GPA (Genetic analysis incorporating Pleiotropy and Annotation)
5 versions - Latest release: 3 months ago - 7.55 thousand downloads total - 15 stars on GitHub - 1 maintainer
PanViz 1.10.0
Integrating Multi-Omic Network Data With Summay-Level GWAS Data
5 versions - Latest release: 3 months ago - 3.25 thousand downloads total - 3 stars on GitHub - 1 maintainer
pathwayPCA 1.24.0
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
5 versions - Latest release: 3 months ago - 1 dependent package - 11.6 thousand downloads total - 11 stars on GitHub - 1 maintainer
GBScleanR 2.2.0
Error correction tool for noisy genotyping by sequencing (GBS) data
9 versions - Latest release: 3 months ago - 6.47 thousand downloads total - 4 stars on GitHub - 1 maintainer
semisup 1.32.0
Semi-Supervised Mixture Model
5 versions - Latest release: 2 months ago - 11.8 thousand downloads total - 1 stars on GitHub - 1 maintainer
GMRP 1.36.0
GWAS-based Mendelian Randomization and Path Analyses
5 versions - Latest release: 3 months ago - 14.1 thousand downloads total - 1 maintainer
mitoClone2 1.14.0
Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Muta...
6 versions - Latest release: 2 months ago - 6.15 thousand downloads total - 1 stars on GitHub - 1 maintainer
BiocOncoTK 1.26.0 removed
Bioconductor components for general cancer genomics
5 versions - Latest release: 8 months ago - 13.4 thousand downloads total - 1 maintainer
Top 9.5% on bioconductor.org
beadarraySNP 1.70.0 removed
Normalization and reporting of Illumina SNP bead arrays
3 versions - Latest release: about 1 year ago - 38.5 thousand downloads total - 1 maintainer
InterMineR 1.26.0 removed
R Interface with InterMine-Powered Databases
4 versions - Latest release: about 1 year ago - 12 thousand downloads total - 17 stars on GitHub - 1 maintainer
Top 8.1% on bioconductor.org
ensemblVEP 1.46.0 removed
R Interface to Ensembl Variant Effect Predictor
3 versions - Latest release: about 1 year ago - 2 dependent packages - 36.7 thousand downloads total - 1 maintainer
genotypeeval 1.31.1 removed
QA/QC of a gVCF or VCF file
1 version - Latest release: almost 2 years ago - 10.4 thousand downloads total - 1 maintainer
Top 5.2% on bioconductor.org
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
Related Keywords
Software 96 Genetics 39 Sequencing 28 GeneticVariability 25 GeneExpression 25 GenomeWideAssociation 23 Microarray 19 VariantAnnotation 16 Regression 15 ImmunoOncology 15 DataImport 14 RNASeq 14 DifferentialExpression 13 CopyNumberVariation 13 MultipleComparison 12 GenomicVariation 11 Preprocessing 10 FunctionalGenomics 10 Clustering 9 Transcription 9 GeneRegulation 8 Visualization 8 QualityControl 7 BiomedicalInformatics 7 Alignment 7 StatisticalMethod 7 Classification 6 DNAMethylation 6 Annotation 6 Coverage 5 SystemsBiology 5 GeneSetEnrichment 5 AlternativeSplicing 5 WholeGenome 5 LinkageDisequilibrium 5 Infrastructure 4 Network 4 PrincipalComponent 4 DimensionReduction 4 Transcriptomics 4 GenePrediction 4 SequenceMatching 4 VariantDetection 4 Proteomics 4 GraphAndNetwork 4 Epigenetics 4 DNASeq 3 SomaticMutation 3 DifferentialSplicing 3 genomics 3 TwoChannel 3 MethylationArray 3 gwas 3 OneChannel 3 ChIPSeq 3 Pathways 3 FunctionalPrediction 3 MethylSeq 3 SingleCell 3 ComparativeGenomics 3 Bayesian 3 HiddenMarkovModel 2 DifferentialMethylation 2 MassSpectrometry 2 aCGH 2 AssayDomain 2 FeatureExtraction 2 KEGG 2 bioconductor-package 2 Reactome 2 bioinformatics 2 Metabolomics 2 qtl 2 r 2 r-package 2 GeneTarget 2 MathematicalBiology 2 Survival 2 MultipleSequenceAlignment 2 GenomeAnnotation 2 WorkflowStep 2 DataRepresentation 2 BatchEffect 2 CpGIsland 2 ExonArray 2 Metagenomics 1 Microbiome 1 NetworkInference 1 TranscriptomeVariant 1 ExomeSeq 1 bayesian 1 IndelDetection 1 GUI 1 Phylogenetics 1 mutation 1 phylogenetics 1 ATACSeq 1 Clustering. 1 BiologicalQuestion 1 GO 1