Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "SNP" keyword
GBScleanR 1.8.0
Error correction tool for noisy genotyping by sequencing (GBS) data3 versions - Latest release: 19 days ago - 2.17 thousand downloads total - 0 stars on GitHub - 1 maintainer
AlphaMissenseR 1.0.0
Accessing AlphaMissense Data Resources in R2 versions - Latest release: 21 days ago - 358 downloads total - 5 stars on GitHub - 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
GGPA 1.14.0
graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architec...3 versions - Latest release: 6 months ago - 4.23 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 7.7% on bioconductor.org
3 versions - Latest release: 6 months ago - 37.4 thousand downloads total - 1 maintainer
CGEN 3.38.0
An R package for analysis of case-control studies in genetic epidemiology3 versions - Latest release: 6 months ago - 37.4 thousand downloads total - 1 maintainer
QTLExperiment 1.0.0
S4 classes for QTL summary statistics and metadata2 versions - Latest release: 7 months ago - 1 dependent package - 840 downloads total - 1 stars on GitHub - 1 maintainer
ISoLDE 1.30.0
Integrative Statistics of alleLe Dependent Expression3 versions - Latest release: 6 months ago - 9.18 thousand downloads total - 1 maintainer
PanViz 1.4.0
Integrating Multi-Omic Network Data With Summay-Level GWAS Data3 versions - Latest release: 6 months ago - 1.66 thousand downloads total - 3 stars on GitHub - 1 maintainer
SICtools 1.32.0
Find SNV/Indel differences between two bam files with near relationship3 versions - Latest release: 6 months ago - 9.24 thousand downloads total - 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
iCNV 1.22.0
Integrated Copy Number Variation detection3 versions - Latest release: 6 months ago - 7.74 thousand downloads total - 1 maintainer
INPower 1.38.0
An R package for computing the number of susceptibility SNPs3 versions - Latest release: 6 months ago - 15.1 thousand downloads total - 1 maintainer
katdetectr 1.4.0
Detection, Characterization and Visualization of Kataegis in Sequencing Data3 versions - Latest release: 6 months ago - 1.91 thousand downloads total - 1 maintainer
hierinf 1.20.0
Hierarchical Inference3 versions - Latest release: 6 months ago - 5.33 thousand downloads total - 1 maintainer
Top 6.2% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 40.9 thousand downloads total - 1 maintainer
logicFS 2.22.0
Identification of SNP Interactions3 versions - Latest release: 6 months ago - 1 dependent package - 40.9 thousand downloads total - 1 maintainer
GPA 1.14.0
GPA (Genetic analysis incorporating Pleiotropy and Annotation)3 versions - Latest release: 6 months ago - 4.2 thousand downloads total - 8 stars on GitHub - 1 maintainer
appreci8R 1.20.2
appreci8R: an R/Bioconductor package for filtering SNVs and short indels with high sensitivity an...4 versions - Latest release: 3 months ago - 7.54 thousand downloads total - 1 maintainer
Top 7.6% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 38.5 thousand downloads total - 1 maintainer
DRIMSeq 1.30.0
Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq3 versions - Latest release: 6 months ago - 1 dependent package - 38.5 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
GIGSEA 1.20.0
Genotype Imputed Gene Set Enrichment Analysis3 versions - Latest release: 6 months ago - 5.56 thousand downloads total - 1 maintainer
hierGWAS 1.32.0
Asessing statistical significance in predictive GWA studies3 versions - Latest release: 6 months ago - 11.7 thousand downloads total - 1 maintainer
Top 8.1% on bioconductor.org
3 versions - Latest release: 6 months ago - 2 dependent packages - 35.3 thousand downloads total - 1 maintainer
ensemblVEP 1.44.0
R Interface to Ensembl Variant Effect Predictor3 versions - Latest release: 6 months ago - 2 dependent packages - 35.3 thousand downloads total - 1 maintainer
iBMQ 1.42.0
integrated Bayesian Modeling of eQTL data3 versions - Latest release: 6 months ago - 16.8 thousand downloads total - 1 maintainer
ASSET 2.20.0
An R package for subset-based association analysis of heterogeneous traits and subtypes3 versions - Latest release: 6 months ago - 1 dependent package - 22 thousand downloads total - 1 maintainer
trigger 1.48.0
Transcriptional Regulatory Inference from Genetics of Gene ExpRession3 versions - Latest release: 6 months ago - 22.3 thousand downloads total - 1 maintainer
trio 3.40.0
Testing of SNPs and SNP Interactions in Case-Parent Trio Studies3 versions - Latest release: 6 months ago - 23.7 thousand downloads total - 1 maintainer
ASAFE 1.28.0
Ancestry Specific Allele Frequency Estimation3 versions - Latest release: 6 months ago - 10.3 thousand downloads total - 1 maintainer
customProDB 1.42.1
Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics ...4 versions - Latest release: 2 months ago - 26 thousand downloads total - 1 maintainer
IMAS 1.26.0
Integrative analysis of Multi-omics data for Alternative Splicing3 versions - Latest release: 6 months ago - 9.74 thousand downloads total - 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
GEM 1.28.0
GEM: fast association study for the interplay of Gene, Environment and Methylation3 versions - Latest release: 6 months ago - 10 thousand downloads total - 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
BiocOncoTK 1.22.2
Bioconductor components for general cancer genomics4 versions - Latest release: about 1 month ago - 9.97 thousand downloads total - 1 maintainer
Top 7.5% on bioconductor.org
3 versions - Latest release: 6 months ago - 40.7 thousand downloads total - 1 maintainer
chopsticks 1.68.0
The 'snp.matrix' and 'X.snp.matrix' Classes3 versions - Latest release: 6 months ago - 40.7 thousand downloads total - 1 maintainer
BG2 1.2.0
Performs Bayesian GWAS analysis for non-Gaussian data using BG23 versions - Latest release: 6 months ago - 1.3 thousand downloads total - 1 maintainer
Top 9.9% on bioconductor.org
3 versions - Latest release: 6 months ago - 26.1 thousand downloads total - 1 maintainer
MassArray 1.54.0
Analytical Tools for MassArray Data3 versions - Latest release: 6 months ago - 26.1 thousand downloads total - 1 maintainer
Top 9.0% on bioconductor.org
3 versions - Latest release: 6 months ago - 27.6 thousand downloads total - 1 maintainer
RLMM 1.64.0
A Genotype Calling Algorithm for Affymetrix SNP Arrays3 versions - Latest release: 6 months ago - 27.6 thousand downloads total - 1 maintainer
iASeq 1.46.0
iASeq: integrating multiple sequencing datasets for detecting allele-specific events3 versions - Latest release: 6 months ago - 21.2 thousand downloads total - 1 maintainer
mbQTL 1.2.0
mbQTL: A package for SNP-Taxa mGWAS analysis3 versions - Latest release: 6 months ago - 1.26 thousand downloads total - 1 maintainer
epistasisGA 1.4.0
An R package to identify multi-snp effects in nuclear family studies using the GADGETS method3 versions - Latest release: 6 months ago - 1.63 thousand downloads total - 1 stars on GitHub - 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
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
SNPediaR 1.28.0
Query data from SNPedia3 versions - Latest release: 6 months ago - 9.71 thousand downloads total - 8 stars on GitHub - 1 maintainer
sitePath 1.18.0
Phylogeny-based sequence clustering with site polymorphism3 versions - Latest release: 6 months ago - 5.09 thousand downloads total - 8 stars on GitHub - 1 maintainer
ProteoDisco 1.8.0
Generation of customized protein variant databases from genomic variants, splice-junctions and ma...3 versions - Latest release: 6 months ago - 2.49 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 9.4% on bioconductor.org
3 versions - Latest release: 6 months ago - 28.5 thousand downloads total - 1 maintainer
GeneRegionScan 1.58.0
GeneRegionScan3 versions - Latest release: 6 months ago - 28.5 thousand downloads total - 1 maintainer
GWAS.BAYES 1.12.0
Bayesian analysis of Gaussian GWAS data3 versions - Latest release: 6 months ago - 3.6 thousand downloads total - 1 maintainer
metaCCA 1.30.0
Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Cano...3 versions - Latest release: 6 months ago - 13.2 thousand downloads total - 1 maintainer
REBET 1.20.0
The subREgion-based BurdEn Test (REBET)3 versions - Latest release: 6 months ago - 5.44 thousand downloads total - 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
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
GMRP 1.30.0
GWAS-based Mendelian Randomization and Path Analyses3 versions - Latest release: 6 months ago - 10.4 thousand downloads total - 1 maintainer
BBCAnalyzer 1.32.0
BBCAnalyzer: an R/Bioconductor package for visualizing base counts3 versions - Latest release: 6 months ago - 12.6 thousand downloads total - 1 maintainer
IVAS 2.22.0
Identification of genetic Variants affecting Alternative Splicing3 versions - Latest release: 6 months ago - 1 dependent package - 14.4 thousand downloads total - 1 maintainer
Top 8.5% on bioconductor.org
3 versions - Latest release: 6 months ago - 2 dependent packages - 33.9 thousand downloads total - 1 maintainer
deepSNV 1.48.0
Detection of subclonal SNVs in deep sequencing data.3 versions - Latest release: 6 months ago - 2 dependent packages - 33.9 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
hapFabia 1.44.0
hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rar...3 versions - Latest release: 6 months ago - 21.5 thousand downloads total - 1 maintainer
Top 1.8% on bioconductor.org
4 versions - Latest release: 16 days ago - 14 dependent packages - 312 thousand downloads total - 2 maintainers
Rsubread 2.18.0
Mapping, quantification and variant analysis of sequencing data4 versions - Latest release: 16 days ago - 14 dependent packages - 312 thousand downloads total - 2 maintainers
Top 0.6% on bioconductor.org
5 versions - Latest release: 19 days ago - 132 dependent packages - 3.56 million downloads total - 1 maintainer
GenomicAlignments 1.40.0
Representation and manipulation of short genomic alignments5 versions - Latest release: 19 days ago - 132 dependent packages - 3.56 million downloads total - 1 maintainer
Top 0.8% on bioconductor.org
5 versions - Latest release: 19 days ago - 129 dependent packages - 2 million downloads total - 1 maintainer
BSgenome 1.72.0
Software infrastructure for efficient representation of full genomes and their SNPs5 versions - Latest release: 19 days ago - 129 dependent packages - 2 million downloads total - 1 maintainer
Top 0.9% on bioconductor.org
4 versions - Latest release: 19 days ago - 93 dependent packages - 1.54 million downloads total - 1 maintainer
VariantAnnotation 1.50.0
Annotation of Genetic Variants4 versions - Latest release: 19 days ago - 93 dependent packages - 1.54 million downloads total - 1 maintainer
Top 5.2% on bioconductor.org
3 versions - Latest release: 9 days ago - 1 dependent package - 55.1 thousand downloads total - 32 stars on GitHub - 1 maintainer
GENESIS 2.34.0
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzi...3 versions - Latest release: 9 days ago - 1 dependent package - 55.1 thousand downloads total - 32 stars on GitHub - 1 maintainer
Top 4.1% on bioconductor.org
3 versions - Latest release: 13 days ago - 4 dependent packages - 95.1 thousand downloads total - 13 stars on GitHub - 1 maintainer
GWASTools 1.50.0
Tools for Genome Wide Association Studies3 versions - Latest release: 13 days ago - 4 dependent packages - 95.1 thousand downloads total - 13 stars on GitHub - 1 maintainer
Top 4.6% on bioconductor.org
3 versions - Latest release: 14 days ago - 1 dependent package - 58.6 thousand downloads total - 3 stars on GitHub - 1 maintainer
SeqVarTools 1.42.0
Tools for variant data3 versions - Latest release: 14 days ago - 1 dependent package - 58.6 thousand downloads total - 3 stars on GitHub - 1 maintainer
InterMineR 1.26.0
R Interface with InterMine-Powered Databases4 versions - Latest release: 12 days ago - 10.4 thousand downloads total - 17 stars on GitHub - 1 maintainer
Top 3.2% on bioconductor.org
3 versions - Latest release: 13 days ago - 11 dependent packages - 368 thousand downloads total - 1 maintainer
oligo 1.68.0
Preprocessing tools for oligonucleotide arrays3 versions - Latest release: 13 days ago - 11 dependent packages - 368 thousand downloads total - 1 maintainer
Top 4.6% on bioconductor.org
3 versions - Latest release: 13 days ago - 3 dependent packages - 63.7 thousand downloads total - 1 maintainer
sangerseqR 1.40.0
Tools for Sanger Sequencing Data in R3 versions - Latest release: 13 days ago - 3 dependent packages - 63.7 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 5.9% on bioconductor.org
3 versions - Latest release: 13 days ago - 3 dependent packages - 204 thousand downloads total - 1 maintainer
systemPipeR 2.10.0
systemPipeR: workflow management and report generation environment3 versions - Latest release: 13 days ago - 3 dependent packages - 204 thousand downloads total - 1 maintainer
mitoClone2 1.10.0
Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Muta...4 versions - Latest release: 13 days ago - 2.32 thousand downloads total - 0 stars on GitHub - 1 maintainer
martini 1.24.0
GWAS Incorporating Networks3 versions - Latest release: 13 days ago - 7.58 thousand downloads total - 4 stars on GitHub - 1 maintainer
cageminer 1.10.0
Candidate Gene Miner3 versions - Latest release: 14 days ago - 2.64 thousand downloads total - 1 stars on GitHub - 1 maintainer
gcatest 2.4.0
Genotype Conditional Association TEST3 versions - Latest release: 16 days ago - 10.7 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 6.9% on bioconductor.org
3 versions - Latest release: 16 days ago - 1 dependent package - 39.3 thousand downloads total - 15 stars on GitHub - 1 maintainer
lfa 2.4.0
Logistic Factor Analysis for Categorical Data3 versions - Latest release: 16 days ago - 1 dependent package - 39.3 thousand downloads total - 15 stars on GitHub - 1 maintainer
VariantFiltering 1.40.0
Filtering of coding and non-coding genetic variants3 versions - Latest release: 20 days ago - 23.6 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 4.6% on bioconductor.org
3 versions - Latest release: 20 days ago - 1 dependent package - 54.2 thousand downloads total - 1 stars on GitHub - 1 maintainer
qpgraph 2.38.0
Estimation of genetic and molecular regulatory networks from high-throughput genomics data3 versions - Latest release: 20 days ago - 1 dependent package - 54.2 thousand downloads total - 1 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
multistateQTL 1.0.0
Toolkit for the analysis of multi-state QTL data1 version - Latest release: 21 days ago - 0 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
Qtlizer 1.16.0
Comprehensive QTL annotation of GWAS results2 versions - Latest release: 6 months ago - 6.25 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
2 versions - Latest release: 6 months ago - 15 dependent packages - 395 thousand downloads total - 1 maintainer
snpStats 1.52.0
SnpMatrix and XSnpMatrix classes and methods2 versions - Latest release: 6 months ago - 15 dependent packages - 395 thousand downloads total - 1 maintainer
OPWeight 1.24.0
Optimal p-value weighting with independent information2 versions - Latest release: 6 months ago - 16.2 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 3.8% on bioconductor.org
2 versions - Latest release: 6 months ago - 6 dependent packages - 430 thousand downloads total - 1 maintainer
siggenes 1.76.0
Multiple Testing using SAM and Efron's Empirical Bayes Approaches2 versions - Latest release: 6 months ago - 6 dependent packages - 430 thousand downloads total - 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
gwasurvivr 1.20.0
gwasurvivr: an R package for genome wide survival analysis2 versions - Latest release: 6 months ago - 9.23 thousand downloads total - 9 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
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
SigsPack 1.16.0
Mutational Signature Estimation for Single Samples2 versions - Latest release: 6 months ago - 4.69 thousand downloads total - 2 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
GeneGeneInteR 1.28.0
Tools for Testing Gene-Gene Interaction at the Gene Level2 versions - Latest release: 6 months ago - 10.3 thousand downloads total - 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
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
genotypeeval 1.31.1 removed
QA/QC of a gVCF or VCF file1 version - Latest release: 7 months ago - 10.4 thousand downloads total - 1 maintainer
Related Keywords
Software
93
Genetics
37
Sequencing
28
GeneticVariability
24
GeneExpression
24
GenomeWideAssociation
22
Microarray
19
VariantAnnotation
16
ImmunoOncology
15
Regression
14
RNASeq
14
DataImport
14
CopyNumberVariation
13
DifferentialExpression
12
MultipleComparison
12
GenomicVariation
10
FunctionalGenomics
9
Transcription
9
Clustering
9
Preprocessing
9
GeneRegulation
8
Alignment
7
BiomedicalInformatics
7
Visualization
7
StatisticalMethod
7
QualityControl
7
DNAMethylation
6
Classification
6
Annotation
6
AlternativeSplicing
5
GeneSetEnrichment
5
LinkageDisequilibrium
5
Coverage
5
WholeGenome
4
GenePrediction
4
SequenceMatching
4
Transcriptomics
4
PrincipalComponent
4
Network
4
GraphAndNetwork
4
SystemsBiology
4
DimensionReduction
4
Infrastructure
4
Proteomics
4
DNASeq
3
SomaticMutation
3
Pathways
3
MethylSeq
3
MethylationArray
3
FunctionalPrediction
3
Bayesian
3
OneChannel
3
ChIPSeq
3
TwoChannel
3
Epigenetics
3
gwas
3
VariantDetection
3
DifferentialSplicing
3
genomics
3
BatchEffect
2
FeatureExtraction
2
bioinformatics
2
ExonArray
2
ComparativeGenomics
2
r
2
r-package
2
aCGH
2
qtl
2
GeneTarget
2
SingleCell
2
GenomeAnnotation
2
bioconductor-package
2
Survival
2
KEGG
2
Metabolomics
2
Reactome
2
WorkflowStep
2
MassSpectrometry
2
MathematicalBiology
2
DataRepresentation
2
CpGIsland
2
AssayDomain
2
HiddenMarkovModel
2
MultipleSequenceAlignment
2
DifferentialMethylation
2
mouse
1
transcription
1
qtl-mapping
1
systemsbiology
1
snp
1
genomicvariation
1
geneticvariability
1
genetics
1
generegulation
1
functionalprediction
1
functionalgenomics
1
functional-variants
1
clustering
1
biomedicalinformatics
1
ReportWriting
1