Bioconductor Packages

Ancestry Specific Allele Frequency Estimation

An R package for subset-based association analysis of heterogeneous traits and subtypes

Accessing AlphaMissense Data Resources in R

BBCAnalyzer: an R/Bioconductor package for visualizing base counts

Performs Bayesian GWAS analysis for non-Gaussian data using BG2

Software infrastructure for efficient representation of full genomes and their SNPs

Case Control Allele Frequency Estimation

An R package for analysis of case-control studies in genetic epidemiology

Summarization and expression/phenotype association of CNV ranges

CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.

Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq

Evaluating SNV-Induced Disruption of G-Quadruplex Structures

Error correction tool for noisy genotyping by sequencing (GBS) data

GEM: fast association study for the interplay of Gene, Environment and Methylation

GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness

graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture

GWAS-based Mendelian Randomization and Path Analyses

GPA (Genetic analysis incorporating Pleiotropy and Annotation)

Bayesian analysis of Gaussian GWAS data

Tools for Genome Wide Association Studies

GeneRegionScan

Representation and manipulation of short genomic alignments

Processing Various Types of Data on GEO and TCGA

Integrative analysis of Multi-omics data for Alternative Splicing

An R package for computing the number of susceptibility SNPs

Integrative Statistics of alleLe Dependent Expression

Identification of genetic Variants affecting Alternative Splicing

MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data

Analytical Tools for MassArray Data

A Package for De Novo CNV Detection in Case-Parent Trios

In-silico methods for genetic finemapping in inbred mice

Standardise summary statistics from GWAS

Optimal p-value weighting with independent information

Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences

S4 classes for QTL summary statistics and metadata

Comprehensive QTL annotation of GWAS results

The subREgion-based BurdEn Test (REBET)

R package for RIVER (RNA-Informed Variant Effect on Regulation)

A Genotype Calling Algorithm for Affymetrix SNP Arrays

Mapping, quantification and variant analysis of sequencing data

SNP Effect Matrix Pipeline in R

Find SNV/Indel differences between two bam files with near relationship

Query data from SNPedia

Tools for variant data

Mutational Signature Estimation for Single Samples

Annotation of Genetic Variants

Filtering of coding and non-coding genetic variants

appreci8R: an R/Bioconductor package for filtering SNVs and short indels with high sensitivity and high PPV

Candidate Gene Miner

The 'snp.matrix' and 'X.snp.matrix' Classes