Bioconductor Packages

Analysis of Alternative Splicing Using RNA-Seq

Manipulation of SQLite-based annotations in Bioconductor

Assess Gene Predictions Using Proteomics and Evolutionary Conservation

R package associated to BREW3R

Forge your own BSgenome data package

Coordinate-Based Genomic Visualization Package for R

Coordinate Covariation Analysis

Methylation array and sequencing spatial analysis methods

DeepBlueR

A unified framework for working transparently with on-disk and in-memory array-like datasets

Making Enriched Heatmaps

Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

Enhanced string parsing for genomic coordinates

GenomicDistributions: fast analysis of genomic intervals with Bioconductor

Query the gene models of a given organism/assembly

Representation and manipulation of genomic intervals

Classification of Helicobacter Pylori Genomes

Grey Lists -- Mask Artefact Regions Based on ChIP Inputs

HDF5 datasets as array-like objects in R

HMMRATAC - a semi-supervised machine learning approach for identifying open chromatin regions from ATAC-Seq data using Hidden Markov Models

Introduce *Ranges to bedtools users

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

Making 2D Hilbert Curve

Interval-Wise Testing for Omics Data

R Interface with InterMine-Powered Databases

Locus overlap analysis for enrichment of genomic ranges

DNA IP-seq data analysis

Methylation-Based Inference of Regulatory Activity

NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment

Optimising the Definition of Expressed Regions

dplyr-based Access to Bioconductor Annotation Resources

piRNA Cluster Builder

Quantitative DNA Sequencing for Chromosomal Aberrations

RBP Inherent Specificity and Variation Sensitivity Analysis Tool

RNA Centric Annotation System

An R package for analysis of massive parallel sequencing based RNA structure probing data

Extraction of Region Properties Features from Interval-based Genomic Data

Extraction of Region Properties Features from Interval-based Genomic Data

Estimates Isoform Specific RPF Footprint Densities

Mapping, quantification and variant analysis of sequencing data

The Genomic STate ANnotation Package

Visualization of genomic structural variants

A simple S4 class for storing basic information about a collection of genomic sequences

A container (S4 class) for matrix-like assays

Promoter identification from large-scale TSS profiling data

Low-level utilities to retrieve data from the UCSC Genome Browser

A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend

Annotation of Genomic Regions to Genomic Annotations

Affinity test for identifying regulatory SNPs

Context-Aware Transcript Quantification from Long Read RNA-Seq data