Monocle 2.1.0 available through GitHub

Monocle 2.1.0 introduces some significant improvements and bugfixes, mainly centered around Census, our algorithm for converting relative expression values to transcript counts.


  • Monocle’s algorithm for converting relative expression values (e.g. TPMs) into absolute transcript counts, called “Census” has been re-designed. The new version is much more accurate. Census is available through the relative2abs() function. The interface to this function has changed, and the output values will be quite different from the old version. The main change is that the version in 1.99.0 reported cDNA counts, as estimated in each cell’s cDNA library. Now, relative2abs reports estimates of mRNA counts in the lysate. These are easier to compare with experiments that estimate mRNA counts via the use of spike-in controls.

  • A new heatmap function plot_pseudotime_heatmap() replaces the old plot_genes_heatmap().

  • Lots of new documentation. More to follow in upcoming releases.


  • Ordering cells with DDRTree no longer compresses cells at the tips of trajectories.

  • Pseudo counts are now applied correctly no matter what the underlying distribution used to model expression is.

  • Variance stabilization is applied correctly when a CellDataSet object’s expressionFamily is negbinomial.size().

  • The gene_id field in results from calculateMarkerSpecificity is now a character instead of a factor. This was leading to indexing errors and nonsensical semi-supervised clustering and ordering results.

  • BEAM() and plot_branched_heatmap() now use cBind instead of cbind, fixing an issue with sparse matrices.

This is the second public release of Monocle 2 through GitHub. You can check out a full list of features here.

To upgrade, please see the getting started page. As usual please report any issues through the issue tracker on the Monocle GitHub page.