Bioconductor Packages

GEM: fast association study for the interplay of Gene, Environment and Methylation

Downloads ENA Fastqs With GEO Accessions

A compilation of metadata from NCBI GEO

Get data from NCBI Gene Expression Omnibus (GEO)

Genomics explorer using statistical and survival analysis in R

Visualise microarray and RNAseq data using gene ontology annotations

GSCA: Gene Set Context Analysis

Defining and visualizing the distances between different genesets

Genomic Visualizations in R

GeneRegionScan

Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

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

Representation and manipulation of short genomic alignments

Enhanced string parsing for genomic coordinates

NIH / NCI Genomic Data Commons Access

GenomicDistributions: fast analysis of genomic intervals with Bioconductor

Query the gene models of a given organism/assembly

Distributed computing by file or by range

Representation and manipulation of genomic intervals

Infrastructure to work with genomewide position-specific scores

Representation and Manipulation of Genomic Tuples

NanoString GeoMx Tools

Population-level Representation on scRNA-Seq data

Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)

S4 Class for Quantitative Data and Associated Networks

Guitar

HDF5 datasets as array-like objects in R

Tools for HELP data analysis

Automated analysis of high-throughput qPCR data

Introduce *Ranges to bedtools users

The Herper package is a simple toolset to install and manage conda packages and environments from R

Framework for Storing and Accessing Hi-C Data Through HDF Files

Bioconductor class for interacting with Hi-C files in R

Parser for HiC data in R

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

HiCaptuRe: Manipulating and integrating Capture Hi-C data

HiCool

Set of 3D genomic interaction analysis tools

R interface to EBI HoloFood resource

Interface to 'HuBMAP'

Utilities to create and use Bioconductor Hubs

ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data

Quality Assessment Tools for Oxford Nanopore MinION data

Foundation of integer range manipulation in Bioconductor

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

Interval-Wise Testing for Omics Data

NPMLE for Censored and Truncated Data

Base Classes for Storing Genomic Interaction Data

Graphical User Interface for IsoCorrectoR

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