Bioconductor Packages

BBCAnalyzer: an R/Bioconductor package for visualizing base counts

Computational pipeline for computing probability of modification from structure probing experiment data

Infers clonal composition of a tumor

Tools for counting and visualising mutations in a target location

Epistasis Analysis for Quantitative Traits by Functional Regression Model

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

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

Gene Set Regulation (GS-Reg)

Tools for Genome Wide Association Studies

Integrative Statistics of alleLe Dependent Expression

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

An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples

Quasispecies Diversity

Robust Ancestry Inference using Data Synthesis

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

A Genotype Calling Algorithm for Affymetrix SNP Arrays

RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

Mapping, quantification and variant analysis of sequencing data

Statistical Inference of Associations between Microbial Communities And host phenoTypes

Tools for variant data

TVTB: The VCF Tool Box

Tools for Exploratory Analysis of Variant Calls

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

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

Detection of subclonal SNVs in deep sequencing data.

An R package to identify multi-snp effects in nuclear family studies using the GADGETS method

Seamless visualization of complex genomic variations in GMOs and edited cell lines

gwasurvivr: an R package for genome wide survival analysis

hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data

GWAS Incorporating Networks

Statistical analysis for sparse high-throughput sequencing

Microbiota STability ASsessment via Iterative cluStering

Microbiome Exploration App

Analysing Illumina HumanMethylation BeadChip Data

Preprocessing and Analysis of Deep Mutational Scanning Data

Cross omic genetic fingerprinting

Handling and analysis of high-throughput microbiome census data

Estimation of Genetic and Molecular Regulatory Networks from High-Throughput Genomics Data

scQTLtools: an R/Bioconductor package for comprehensive identification and visualization of single-cell eQTLs

SnpMatrix and XSnpMatrix classes and methods

Testing of SNPs and SNP Interactions in Case-Parent Trio Studies