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dyngen: a multi-modal simulator for spearheading new single-cell omics analyses

Simulate gene regulation, splicing and translation at a single cell, single molecule level.

The Rockerverse: Packages and Applications for Containerization with R

A survey of projects building upon Rocker and presents the current state of R packages for managing Docker images and controlling containers.

The RNA Atlas, a single nucleotide resolution map of the human transcriptome

A comprehensive atlas of the human transcriptome that is derived from matching polyA-, total-, and small-RNA profiles of a heterogeneous collection of nearly 300 human tissues and cell lines.

Trajectory-based differential expression analysis for single-cell sequencing data

A powerful framework for inferring within-lineage and between-lineage differential expression.

A comparison of single-cell trajectory inference methods: towards more accurate and robust tools

The first comprehensive assessment of trajectory inference methods.

SCORPIUS improves trajectory inference and identifies novel modules in dendritic cell development

SCORPIUS improves trajectory inference and identifies novel modules in dendritic cell development