Bioconductor Packages

Ancestry Specific Allele Frequency Estimation

Package for CTDbase data query, visualization and downstream analysis

R interface to a subset of OpenBabel functionalities

Cheminformatics Toolkit for R

Clustering of Immune Receptor Repertoires

Differential Binding Analysis of ChIP-Seq Peak Data

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

Expression Weighted Celltype Enrichment

Prediction of gestational age with Illumina HumanMethylation450 data

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

Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies

Differential gene usage in immune repertoires

Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data

Longitudinal Analysis of Cancer Evolution (LACE)

Muscle Epigenetic Age Test

MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks

In-silico methods for genetic finemapping in inbred mice

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

Optimal p-value weighting with independent information

A tool to identify potentially oncogenic genes

PhenoGeneRanker: A gene and phenotype prioritization tool

Infers biological signatures from gene expression data

RESOLVE: An R package for the efficient analysis of mutational signatures from cancer genomes

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

RImmPort: Enabling Ready-for-analysis Immunology Research Data

Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

Spatial Image Analysis of Tissues

Calculate Pathway Scores for Each Cell in scRNA-Seq Data

Mutational Signature Estimation for Single Samples

SparseSignatures

R package for TENET (Tracing regulatory Element Networks using Epigenetic Traits) to identify key transcription factors

TRONCO, an R package for TRanslational ONCOlogy

Viral Evolution ReconStructiOn (VERSO)

Package for prediction of zygosity for variants/genes in NGS data

Analytical R tools for Mass Spectrometry

Within And Between Batch Correction Of LC-MS Metabolomics Data

A Hidden Markov Model Approach for Identifying Differentially Methylated Sites and Regions for Beta-Valued DNA Methylation Data

Automated functions for comparing various omic data from cbioportal.org

Informatics Tools for Cell-Free DNA Study

Codon Usage Analysis and Prediction of Gene Expressivity

Differential Expression Analysis for RNA-seq data through a robust variance component test

Decomposition of individual tumors into mutational signatures by signature refitting

Drug-Target Interactions

Estimate Systems Immune Response from RNA-seq data

Empirical Analysis of Digital Gene Expression Data in R

Accelerated similarity searching of small molecules

R interface for FDA Adverse Event Reporting System

Automatic and interactive quality control for flow cytometry data

Mismatch Tolerant Maximum Common Substructure Searching