cellula

cellula is a simple R-based pipeline for single cell RNA-seq processing with a number of methods for integration and identity assignment.

You can read all about it on the companion website!

Changelog

• 23/3/2025:
  Various bug fixes

• 13/3/2025:
  Added heatmap plotting and proportion plotting functions

• 8/3/2025:
  Added pseudobulk DE functions for analysis and plotting

• 4/3/2025:
  Added integration diagnostics

• 29/10/2024:
  Added stacked violin plots and multipanel dimensionality reduction plots

• 29/1/2024:
  Added additional methods for integration: scMerge2 from scMerge and STACAS from STACAS

• 30/7/2023:
  Added a function to build references for the Jaitin method from a SCE. Fixed minor bugs in identity assignment

• 23/7/2023:
  Added several options for color palettes by overhauling color management.

• 21/7/2023:
  Moved many optional dependencies in Suggests in DESCRIPTION, added cell cycle estimation and visualization

• 15/6/2023:
  Added a new fast method for identity assignment based on a reference (Jaitin method)

• 3/6/2023:
  Added interface to monocle3 trajectory inference and a new UMAP embedding