Bioconductor Packages

Infers clonal composition of a tumor

Clustering of MS2 Spectra for Metabolite Identification

Data for the CluMSID package

ClustAll: Data driven strategy to robustly identify stratification of patients within complex diseases

Clustering of Immune Receptor Repertoires

Calculate similarity of clusters from different single cell samples using foldchanges

Judging Quality of Clustering Methods using Mutual Information

The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data

Coordinated Gene Activity in Pattern Sets

VST normalized RNA-Sequencing data with annotations for multiple species samples from Bgee

Functional connections between drugs, genes and diseases as revealed by common gene-expression changes

ConsensusClusterPlus

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

Classes and Functions to Serve as the Basis for Other 'Gx' Packages

An R package for colorectal cancer screening and microbiome analysis

Queries the Human Cell Atlas

Power analysis for CyTOF experiments

Robust prediction of clinical outcomes using cytometry data without cell gating

Conditional Differential Analysis for Flow and Mass Cytometry Experiments

Low Dimensions projection of cytometry samples

DNA methylation-based machine learning models

Data accompanying the DAPAR and Prostar packages

Denoising Algorithm based on Relevance network Topology

Tools for curating, analyzing, and manipulating biological sequences

Two-sample tests on a graph

Differential gene expression analysis based on the negative binomial distribution

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

Differential Expression Meta-Analysis

Data package for DExMA package

Diffuse large B-cell lymphoma expression data

Differentially Methylated Cytosines via a Bayesian Functional Approach

Differentially Methylated CpG using Hidden Markov Model

Methylation array and sequencing spatial analysis methods

Data Package for DMRcate

Example DNAm Data for DMRsegal

DNA Zoo data package

DNA Cyclizability Prediction

Differential Network Enrichment Analysis for Biological Data

Genome-wide Detection of Differential ORF Usage

Convenient functions to streamline your single cell data analysis workflow

Data Mining for RNA-seq data: normalization, feature selection and classification

DeMAND

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

Poor prognosis colon cancer is defined by a molecularly distinct subtype and precursor lesion

Protein Interactions and Networks with Compounds based on Sequences using Deep Learning

R package for sparse and out-of-core arithmetic and decomposition of Tensor

Inferring tumor-specific cancer dependencies through integrating ex-vivo drug response assays and drug-protein profiling

Differentially regulated genes from scRNA-seq data

Normalization of Single-Cell mRNA Sequencing Data

Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data