Bioconductor Packages

A toolkit for APA analysis using RNA-seq data

visualization and annotation of isotopic enrichment patterns of peptides and metabolites with stable isotope labeling from proteomics and metabolomics

Accessing AlphaMissense Data Resources in R

Manipulation of SQLite-based annotations in Bioconductor

Facilities for Filtering Bioconductor Annotation Resources

Tools for building SQLite-based annotation data packages

Software infrastructure for efficient representation of full genomes and their SNPs

Forge your own BSgenome data package

Code for using BridgeDb identifier mapping framework from within R

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

Category Analysis

Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

Analysis of single-cell epigenomics datasets with a Shiny App

Creating and Using (Chemical) Compound Annotation Databases

Coralysis sensitive identification of imbalanced cell types and states in single-cell data via multi-level integration

Disease Ontology Semantic and Enrichment analysis

Convenient functions to streamline your single cell data analysis workflow

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

a Global Weighted Model for Disease Ontology Enrichment Analysis

Functional Gene Networks derived from biological enrichment analyses

find influential TF and Target based on multi-omics data

GO-terms Semantic Similarity Measures

Visualise microarray and RNAseq data using gene ontology annotations

Sunburst Plot for Enriched Gene Ontology Terms

Find the most characteristic gene ontology terms for groups of human genes

Tools for manipulating GO and microarrays

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

Query the gene models of a given organism/assembly

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

HDF5 datasets as array-like objects in R

Introduce *Ranges to bedtools users

Methods for BCR single-cell embedding

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

Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)

DBI to construct MeSH-related package from sqlite file

Calculate, visualize and analyse overlap between genomic regions

R wrapper for the OMA REST API

OmniPath web service client and more

dplyr-based Access to Bioconductor Annotation Resources

Software to enable the smooth interfacing of different database packages

Phenotype Consensus ANalysis (PCAN)

Rank-based reference mapping for fast and robust cell type annotation in spatial and single-cell transcriptomics

Reactome Pathway Analysis

Transform and Filter SWATH Data for Statistical Packages

Information Accretion-based Function Predictor Evaluation