Bioconductor packages

Calibration curves for targeted proteomics, lipidomics and metabolomics data

A mass spectrometry imaging toolbox for statistical analysis

Read and write mass spectrometry imaging files

Category Analysis

This package provides methods for analysing spatial transcriptomics data and for discovering gene clusters

Causal network analysis methods

Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis

Cellular DNA Barcode Analysis toolkit

Construct Benchmarks for Single Cell Analysis Methods

Predict genes expressed selectively in specific cell types

Supervised Non-negative Matrix Factorization for Dimensional Reduction in Single-Cell Analysis

Evaluate Cellspecific Mixing

Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

Reconstruction, visualization and analysis of branching trajectories

Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis

Cepo for the identification of differentially stable genes

An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

Quantitative comparison of multiple ChIP-seq datasets

Quality metrics for ChIPseq data

ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles

ChIPanalyser: Predicting Transcription Factor Binding Sites

ChIPexoQual

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

Identifying Protein Binding Sites in High-Throughput Sequencing Data

Simulation of ChIP-seq experiments

R interface to a subset of OpenBabel functionalities

Cheminformatics Toolkit for R

CHiCAGO: Capture Hi-C Analysis of Genomic Organization

Heat map plotting by genome coordinate

Analysis of single-cell epigenomics datasets with a Shiny App

Infrastructure for Chromatographic Mass Spectrometry Data

End-to-End Analysis of Small RNA-Seq Data from Viroids

CiteFuse: multi-modal analysis of CITE-seq data

A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing

Detect and Correct Genomic DNA Contamination in RNA-seq Data

Infers clonal composition of a tumor

Simulation of Tumor Clonal Evolution with Realistic Sequencing Noise

Clustering of MS2 Spectra for Metabolite Identification

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

One-Step to Cluster and Visualize Gene Expression Data

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

Different test statistics based on co-citation.

Coordinated Gene Activity in Pattern Sets

An Investigation Across Different Species and Tissues

Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic and epigenomic data sets