Bioconductor Packages

Attribute-Weighted Aggregation

A Functional Approach To Impute Genetically Regulated Expression

Model higher-order methylation profiles

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

Statistical analysis for the Colony Formation Assay

Identification of cell-type-specific spatially variable genes accounting for excess zeros

Calibration curves for targeted proteomics, lipidomics and metabolomics data

A mass spectrometry imaging toolbox for statistical analysis

Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis

Robust prediction of clinical outcomes using cytometry data without cell gating

Conditional Differential Analysis for Flow and Mass Cytometry Experiments

Differential gene expression analysis based on the negative binomial distribution

Differentially Methylated Cytosines via a Bayesian Functional Approach

Genome-wide Detection of Differential ORF Usage

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

Normalization of Single-Cell mRNA Sequencing Data

A DownStream Chemo-Proteomics Analysis Pipeline

Quality control and analysis tools for Illumina DNA methylation BeadChip

Graphical Exploration of Design Matrices

Exposure-Aware Multi-Omics Risk Modeling

Prediction of gestational age with Illumina HumanMethylation450 data

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

GEne Network Inference with Ensemble of trees

GWAS-based Mendelian Randomization and Path Analyses

Constructing gene regulatory networks from expression data through functional module inference

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

Delineate outstanding genomic zones of differential gene activity

Global test for groups of variables via model comparisons

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

Robust Inference for Absolute Abundance in Microbiome Analysis

Integrative analysis of Multi-omics data for Alternative Splicing

Identification of genetic Variants affecting Alternative Splicing

Differential gene usage in immune repertoires

Inference of gene regulatory networks from gene expression data

LEA: an R package for Landscape and Ecological Association Studies

Differential Expression Analysis with Long Read RNA-Seq Data

Differential cell type change analysis using Logistic/linear Regression

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

Multi Omics Survival Clip

Statistical Methods for Chemoproteomics Dose-Response Analysis

Bayesian clustering and imputationa of single cell methylomes

Inferring metabolic networks from untargeted high-resolution mass spectrometry data

Assessing the regulatory potential of DNA methylation regions or sites on gene transcription

Negative binomial model for scRNA-seq

Analysis of OpenArray PCR Data

Optimal p-value weighting with independent information

Tools for Omics Data Analysis

Peptide Set Test

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

A reweighted Lasso-Cox by integrating gene interaction information