Bioconductor Packages

Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

Accessing AlphaMissense Data Resources in R

Basic peak calling on STARR-seq data

Binding site defintion based on iCLIP data

Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

Coordinate Covariation Analysis

An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates

Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic and epigenomic data sets

Differential Expressed Windows Based on Negative Binomial Distribution

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

Differential Binding Analysis of ChIP-Seq Peak Data

Extending guilt by association by degree

Expression Weighted Celltype Enrichment

Comparison, Benchmarking & QC of Epigenomic Datasets

Functional Gene Networks derived from biological enrichment analyses

Gene Set Variation Analysis for Microarray and RNA-Seq Data

Compute the automorphisms between DNA's Abelian group representations

GenomicDistributions: fast analysis of genomic intervals with Bioconductor

Delineate outstanding genomic zones of differential gene activity

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

Comparative analysis of RNA-seq data for hybrids and their progenitors

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

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

Locus overlap analysis for enrichment of genomic ranges

Methylation-Based Inference of Regulatory Activity

Integrate microRNA and gene expression to decipher pathway complexity

Multi Omic Master Regulator Analysis

Modifying splice site usage by changing the mRNP code, while maintaining the genetic code

Benchmarking Epigenomic Profiling Methods Using Motif Enrichment

In-silico methods for genetic finemapping in inbred mice

Compute gene set scores from a deep learning framework

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

Open Reading Frames in Genomics

R wrapper for the OMA REST API

S4 classes for QTL summary statistics and metadata

Rapid Integration of Term Annotation and Network resources

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

Surface Protein Prediction and Identification

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

VarCon: an R package for retrieving neighboring nucleotides of an SNV

Differential cell-type-specific allelic imbalance

Annotation of Genomic Regions to Genomic Annotations

Analysis of Transposable Elements

Candidate Gene Miner

Gene Set Enrichment For ChIP-seq Peak Data

Companion package to chipenrich

Global visualization tool of genomic data

Systematic quality checks on comparative genomics analyses

Base functions and classes for CRISPR gRNA design

Bowtie-based alignment of CRISPR gRNA spacer sequences