Bioconductor Packages

Create Copy-Number Plots using karyoploteR functionality

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

Correlation Motif Fit

Tools for counting and visualising mutations in a target location

Queries the Human Cell Atlas

Finds DAMEs - Differential Allelicly MEthylated regions

Denoising Algorithm based on Relevance network Topology

Tools for curating, analyzing, and manipulating biological sequences

Differential gene expression data formats converter

Two-sample tests on a graph

Report of DEG analysis

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

Orchestrating Blood Radiation Transcriptomic 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