Bioconductor Packages

Differentially Methylated Cytosines via a Bayesian Functional Approach

Differentially Methylated CpG using Hidden Markov Model

Methylation array and sequencing spatial analysis methods

DNA Cyclizability Prediction

Differential Network Enrichment Analysis for Biological Data

Genome-wide Detection of Differential ORF Usage

Convenient functions to streamline your single cell data analysis workflow

Data Mining for RNA-seq data: normalization, feature selection and classification

DeMAND

Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms

Protein Interactions and Networks with Compounds based on Sequences using Deep Learning

R package for sparse and out-of-core arithmetic and decomposition of Tensor

Inferring tumor-specific cancer dependencies through integrating ex-vivo drug response assays and drug-protein profiling

Differentially regulated genes from scRNA-seq data

Normalization of Single-Cell mRNA Sequencing Data

Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data

Interactive Workflow for Discovering Rhythmicity in Biological Data

A DownStream Chemo-Proteomics Analysis Pipeline

Comparison of disease and drug profiles using Gene set Enrichment Analysis

Improving replicability in single-cell RNA-Seq cell type discovery

Analysis of the data from RNA duplex probing experiments

An R package for gene and isoform differential expression analysis of RNA-seq data

Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification

EBcoexpress for Differential Co-Expression Analysis

Extending guilt by association by degree

Ensemble of Gene Set Enrichment Analyses

An R Package for Estimating Copy Number Levels of Viral Genome Segments Using Base-Resolution Read Depth Profile

Quality control and analysis tools for Illumina DNA methylation BeadChip

Uses Brown's method to combine p-values from dependent tests

Predicting Disease Progression Based on Methylation Correlated Blocks using Ensemble Models

Seamless navigation through combined results of set-based and network-based enrichment analysis

An effective identification of alternative splicing events using junction arrays and RNA-Seq data

Graphical Exploration of Design Matrices

Exposure-Aware Multi-Omics Risk Modeling

FEAture SelcTion (FEAST) for Single-cell clustering

Interpretation and enrichment for metabolomics data

Functional Gene Networks derived from biological enrichment analyses

FeatSeekR an R package for unsupervised feature selection

Multidimensional Scaling with F-ratio for microbiome visualization

Using self-organizing maps for visualization and interpretation of cytometry data

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