Single-cell Analysis / R package
tradeSeq
Fit smooth gene expression trends along inferred trajectories and compare patterns between branches.
Best fit
R analysts following up a trajectory fit with tests for changing expression.
What you need
R and Bioconductor, count data, pseudotime values, and lineage weights.
What to check
Associations are conditional on the trajectory. Errors in the inferred ordering can carry into expression tests.