Bioconductor Packages

Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing

EnsDbs for AnnotationHub

Analysis of Alternative Splicing Using RNA-Seq

ATAC-seq Quality Control

BBCAnalyzer: an R/Bioconductor package for visualizing base counts

Model higher-order methylation profiles

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

BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage

Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data

Basic peak calling on STARR-seq data

Binding site defintion based on iCLIP data

Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

A normalization method for Copy Number Aberration in cancer samples

Reliable CNV detection in targeted sequencing applications

CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.

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

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

ChIPanalyser: Predicting Transcription Factor Binding Sites

ChIPexoQual

Simulation of Tumor Clonal Evolution with Realistic Sequencing Noise

Create Copy-Number Plots using karyoploteR functionality

Finds DAMEs - Differential Allelicly MEthylated regions

Differential Enrichment Scan 2

Differentially Methylated Cytosines via a Bayesian Functional Approach

Differentially Methylated CpG using Hidden Markov Model

Differentially Methylated Regions Caller

Methylation array and sequencing spatial analysis methods

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

Utilities for Handling Single-Cell Droplet Data

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

Making Enriched Heatmaps

Find RAre Splicing Events in RNA-Seq Data

Representation and manipulation of short genomic alignments

GenomicDistributions: fast analysis of genomic intervals with Bioconductor

Distributed computing by file or by range

Delineate outstanding genomic zones of differential gene activity

Plot profiles of next generation sequencing data in genomic features

Representation and manipulation of genomic intervals

Infrastructure to work with genomewide position-specific scores

Grey Lists -- Mask Artefact Regions Based on ChIP Inputs

HDF5 datasets as array-like objects in R

Introduce *Ranges to bedtools users

Making 2D Hilbert Curve

Intron-Exon Retention Estimator

Detection of de novo deletion in targeted sequencing trios

DNA IP-seq data analysis

MICSQTL (Multi-omic deconvolution, Integration and Cell-type-specific Quantitative Trait Loci)

Methylation-Based Inference of Regulatory Activity

Prioritization of potentially bioactive metabolic features from epidemiological and environmental metabolomics datasets

Bayesian clustering and imputationa of single cell methylomes