Software
 CrossTalkeRCrossTalkeR is a framework for network analysis and visualisation of LR networks. CrossTalkeR identifies relevant ligands, receptors and cell types contributing to changes in cell communication when contrasting two biological states: disease vs. homeostasis. A case study on scRNA-seq of human myeloproliferative neoplasms reinforces the strengths of CrossTalkeR for characterisation of changes in cellular crosstalk in disease state. See our webpage. |
 MOJITOO : a fast and universal method for integration of multimodal single cell data. MOJITOO uses canonical correlation analysis for a fast and parameter free detection of a shared representation of cells from multimodal single cell data. Moreover, estimated canonical components can be used for interpretation, i.e. association of modality specific molecular features with the latent space. |
 HINT & HINT-ATACHINT (Hmm-based IdeNtification of Transcription factor footprints) is an hmm-based framework that uses open chromatin data (DNase-seq, ATAC-seq and histone modification ChIP-seq) in order to find transcription factor footprints in the DNA. HINT makes part of the Regulatory Genomics Toolbox suite. Please find more information about the tool in the RGT website. |
 Regulatory Genomics ToolboxRegGen is a toolbox for the integrative analysis of regulatory and expression data from ChIP-Seq, RNA-Seq and biological sequences. The tool provides several functionalities required for regulatory analysis as Chip-Seq peak calling, transcription factor binding site detection and association to further experimental data as gene expression. |
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| ODIN and THOR are HMM-based approach to detect and analyse differential peaks in pairs of ChIP-seq data. ODIN is the first differential peak caller that performs genomic signal processing, peak calling and p-value calculation in an integrated framework. THOR extends ODIN by supporting replicates and further normalization approaches. |
 Graphical Query LanguageGQL is a suite of tools for analyizing time-course experiments. Currently, it is adapted to gene expression data. The two main tools are GQLQuery, for querying data sets, and GQLCluster, which provides a way for computing groupings based on a number of methods (model-based clustering using HMMs as cluster models and estimation of a mixture of HMMs). |
Contributed Software
Clever – Click Enumerating Variant Finder
Pymix – Mixture model estimation package in python.
GHMM – A General Hidden Markov Model library in C.