Bioconductor Packages

A Correlation Based Multiview Self Organizing Maps Clustering For IMC Datasets

GARS: Genetic Algorithm for the identification of Robust Subsets of variables in high-dimensional and challenging datasets

Prediction of gestational age with Illumina HumanMethylation450 data

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

GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC

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

GEne Network Inference with Ensemble of trees

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

GWAS-based Mendelian Randomization and Path Analyses

Constructing gene regulatory networks from expression data through functional module inference

Genomics explorer using statistical and survival analysis in R

A set of annotation maps describing the entire Gene Ontology

GO-terms Semantic Similarity Measures

Visualise microarray and RNAseq data using gene ontology annotations

Find the most characteristic gene ontology terms for groups of human genes

Tools for manipulating GO and microarrays

GPA (Genetic analysis incorporating Pleiotropy and Annotation)

Gene Regulatory Network Inference Using Time Series

GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using single-cell or bulk chromatin accessibility and RNA-seq data

Calculate growth-rate inhibition (GR) metrics

Gene Set Analysis in R

Gene set enrichment data structures and methods

Reproducible GSEA Benchmarking

Make Biological Sense of Gene Set Enrichment Analysis Outputs

An Evolutionary Framework for the Identification and Study of Prognostic Gene Expression Signatures in Cancer

Bayesian analysis of Gaussian GWAS data

Pipeline for augmented co-expression analysis

Projection-based Gating Strategy Optimization for Flow and Mass Cytometry

Defining and visualizing the distances between different genesets

Genomic Visualizations in R

GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-seq data and Gene Expression Data

Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

Delineate outstanding genomic zones of differential gene activity

Interpretation of RNA-seq experiments through robust, efficient comparison to public databases

Global test for groups of variables via model comparisons

Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)

Classification of Helicobacter Pylori Genomes

Graph Theoretic Association Tests

GraphAlignment

A set of annotation maps describing the entire Human Disease Ontology

Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD)

A fast hierarchical graph-based clustering method

HLA Genotype Imputation with Attribute Bagging

Heterogeneity-Induced Pre-Processing tOol

Detection of cell-type-specific risk-CpG sites in epigenome-wide association studies

A set of annotation maps describing the entire Human Phenotype Ontology

The removal of batch effects from datasets using a PCA and constrained optimisation based technique

A/B compartment detection and differential analysis

HiCPotts: Hierarchical Modeling to Identify and Correct Genomic Biases in Hi-C