The Rockerverse: Packages and Applications for Containerisation with R

A surveys of projects that build upon the Rocker Project images and presents the current state of R packages for managing Docker images and controlling containers

TinGa: fast and flexible trajectory inference with Growing Neural Gas

TinGa, a new TI model that is fast and flexible, and that is based on Growing Neural Graphs.

A scalable SCENIC workflow for single-cell gene regulatory network analysis

How to perform a fast SCENIC analysis alongside standard best practices steps on single-cell RNA-sequencing data.

Flexible inference of both within-lineage and between-lineage differential expression.

Discover genes associated with dynamic biological processes.

Essential guidelines for computational method benchmarking

A summary of key practical guidelines and recommendations for performing high-quality benchmarking analyses.

A comparison of single-cell trajectory inference methods

Unsure which trajectory inference method to use for your single-cell dataset? Our benchmarking effort sheds light on this matter.

Network Inference from Single-Cell Transcriptomic Data

A discussion on the advantages of performing network inference with single-cell transcriptomics data.

The Transcription Factor ZEB2 Is Required to Maintain the Tissue-Specific Identities of Macrophages

We show ZEB2 is highly expressed across the macrophage lineage.

IncGraph: Incremental graphlet counting for topology optimisation

IncGraph is a method for calculating the differences in graphlet counts with respect to the network in its previous state.

A comprehensive evaluation of module detection methods for gene expression data

A comprehensive and robust evaluation of module detection methods, which group genes into co-expression modules.