MERLot is a tool that can reconstruct the lineage tree topology that explains the emergence of different cell types from a progenitor population. MERLot is an R package than can reconstruct complex lineage tree topologies using coordinates for cells in a given manifold(like diffusion maps) as input.

MERLoT depends on certain R packages in order to work properly. Most of the packages can be installed either via CRAN (with the install.packages() function) or via Bioconductor.

• car
• rgl
• igraph
• fields
• ElPiGraph.r
• FactoMineR
• mclust

The Destiny package for creating diffusion maps was one of the dinmensionality reduction techniques we used in order to reconstruct lineage tree topologies in a low dimensional manifold.

The destiny package as well as instructions about how to install and use it can be found here

Optional packages:

• energy (needed for finding differentially expressed genes)
• VGAM

ElPiGraph.R can be installed following the instructions from the developer's site.

install.packages("devtools") library(devtools) install.packages(c("bigpca", "irlba", "nsprcomp", "plotly","fields", "igraph", "rgl", "tictoc"))

Either download the latest version from the git repository with git clone https://github.com/soedinglab/merlot.git or download one of our releases and unpack it. Then, in R, call:

install.packages("/path/to/merlot/folder", types="source", repos = NULL)

library(devtools)

install_github("soedinglab/merlot")

The rgl library requires an X server to be present. Installing xquartz fixed this for us.