Bioconductor Packages

Identify Differentially Expressed Genes from RNA-seq data

Identifies differentially expressed genes with respect to other local genes

Differential Enrichment Scan 2

Differential gene expression analysis based on the negative binomial distribution

Differential Expressed Windows Based on Negative Binomial Distribution

Inference of differential exon usage in RNA-Seq

a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.

DEsingle for detecting three types of differential expression in single-cell RNA-seq data

DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments

Differential Expression Meta-Analysis

Gene Selection

Differentially Methylated Cytosines via a Bayesian Functional Approach

Differentially Methylated CpG using Hidden Markov Model

Differentially Methylated Regions Caller

Methylation array and sequencing spatial analysis methods

Identification of gene fusions using paired-end sequencing

High-throughput prediction of DNA shape features

Differential Network Enrichment Analysis for Biological Data

Disease Ontology Semantic and Enrichment analysis

Genome-wide Detection of Differential ORF Usage

Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq

Dynamic Transcriptome Analysis

Damsel: an end to end analysis of DamID

DeMAND

Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms

Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data

DeeDeeExperiment: An S4 Class for managing and exploring omics analysis results

Deep characterization of cancer drugs

Probabilistic association of DEGs to CREs from differential data

DegNorm: degradation normalization for RNA-seq data

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

Differential Binding Analysis of ChIP-Seq Peak Data

DiffLogo: A comparative visualisation of biooligomer motifs

Differentially regulated genes from scRNA-seq data

Identification and Annotation of Protein Hotspot Residues

Utilities for Handling Single-Cell Droplet Data

Estimating Absolute Abundance from Microbial Spike-in Controls

Analysis of the data from RNA duplex probing experiments

Exon Based Strategy for Expression Analysis of genes

An R package for gene and isoform differential expression analysis of RNA-seq data

Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification

Exploratory Data Analysis and Normalization for RNA-Seq

Query the EDIR Database For Specific Gene

Extending guilt by association by degree

Ensemble of Gene Set Enrichment Analyses

Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

An R Package for Estimating Copy Number Levels of Viral Genome Segments Using Base-Resolution Read Depth Profile

Earth Mover's Distance for Differential Analysis of Genomics Data

Quality control and analysis tools for Illumina DNA methylation BeadChip

Empirical RNA-seq Sample Size Analysis