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 Covariation Analysis

Methylation array and sequencing spatial analysis methods

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

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

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

dplyr-based Access to Bioconductor Annotation Resources

piRNA Cluster Builder

Quantitative DNA Sequencing for Chromosomal Aberrations

RNA Centric Annotation System

Mapping, quantification and variant analysis of sequencing data

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

A container (S4 class) for matrix-like assays

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

Prediction of intronic splicing branchpoints

Tools for computational epigenomics

fcScan for detecting clusters of coordinates with user defined options

GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction

Optimized Functional Annotation Of ChIP-seq Data

Methylated CpGs Set Enrichment Analysis

Data and functions for dealing with microRNAs

Generation of null ranges via bootstrapping or covariate matching

Identification and classification of plant transcription factors

Coordinate-Based Genomic Visualization Package for R

Data masks for SummarizedExperiment enabling dplyr-like manipulation

Pooling RNA-seq datasets for assembling transcript models

GREAT Analysis - Functional Enrichment on Genomic Regions