hms-dbmi / crestree

Neural Crest Fate Decisions

crestree

A set of methods developed to model cell fate decision landscape of early mouse neural crest.

A walkthrough guide for modelling transcriptional tree is described in https://github.com/hms-dbmi/crestree/blob/master/vignettes/tree_guide.md

Analysis of bifurcation point, using sensory-autonomic bifurcation as example, is described in https://github.com/hms-dbmi/crestree/blob/master/vignettes/bifurcation_point.md

Installation instructions

install.packages("devtools")
devtools::install_github("hms-dbmi/crestree")
library(crestree)

crestree's Issues

Using Crestree

Hello,

Thank you for developing such a great tool. I would like to implement it on my own data. I am trying to understand the input and I am wondering whether you can help me figure it out. I processed my data with Seurat and have a Seurat object.

fpm: Is is the normalized count matrix?
wgm: What is this exactly and how can I get it?
emb: I am using both UMAP and tSNE for visualization. How can I extract this information/coordinates from Seurat object to use as input for emb?

Thank you.