Bioconductor Packages

Provides access to pathogen annotation resources available on EuPathDB databases

Client to access ExperimentHub resources

Add resources to ExperimentHub

Manages subsets of data with Bioconductor Experiment objects

FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data

A Bioconductor package for accessing GA4GH API data servers

Shiny application for interacting with GA4GH-based data servers

Tools for working with gcloud and gsutil

Representing GDS files as array-like objects

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

A set of annotation maps describing the entire Gene Ontology

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

A set of annotation maps describing the entire Human Disease Ontology

Tools for HELP data analysis

A set of annotation maps describing the entire Human Phenotype Ontology

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