Softwares

R

• ClusterDE: a post-clustering differential expression (DE) method robust to false-positive inflation caused by double dipping
• PseudotimeDE: a robust method that accounts for the uncertainty in pseudotime inference and thus identifies DE genes along cell pseudotime with well-calibrated p-values
• scDesign3: an all-in-one single-cell data simulation tool by using reference datasets with different cell states (cell types, trajectories or and spatial coordinates), different modalities, and complex experimental designs
• scPNMF: a dimensionality reduction method to facilitate gene selection for targeted gene profiling by learning a sparse gene encoding of single cells

Python

• scSampler: a tool for fast diversity-preserving subsampling of large-scale single-cell transcriptomic data