read me file 

Single cell RNA-seq data sets: 

WT_01, WT_02 and ZC3H20_KO data sets have been provided as filtered counts matrices in csv files. 

Scripts
These can be used with scripts provided. 
"WT_differentiation_analysis" must be run first in order to integrate WT replicate experiments. The output Seurat object can then be used for WT cell cycle analysis or ZC3H20 KO analysis, in any order.
 

Additional files:

Cell_cycle_regulated_genes - cell cycle phase marker genes (Archer et al 2011)
VSG_list - list of VSGs in the t. brucei genome
bar_height_map.R - custom function for plotting cell cycle gene expression heatmap. 


Software installation and versions tested


# install.packages("BiocManager") v1.30.1
#install.packages("devtools") v2.3.2
#install.packages('Seurat') v3.2.2.99
#BiocManager::install("scran") v1.14.6
#BiocManager::install("scater") v1.14.6
#BiocManager::install("MAST") v1.12.0
#BiocManager::install("SingleCellExperiment") v1.8.0
#BiocManager::install("slingshot") v1.4.0
#BiocManager::install("tradeSeq") v1.3.21
#BiocManager::install("clusterExperiment") v2.6.1
#BiocManager::install("ggpubr") v0.4.0
#BiocManager::install("clustree") v0.4.3 
#BiocManager::install("mgcv") v1.8-34
# For phate, first install phateR python package - https://github.com/KrishnaswamyLab/phateR
#install.packages("phateR") 1.0.7
#BiocManager::install("ComplexHeatmap") v2.2.0
#remotes::install_github("carmonalab/STACAS") v1.0.1
#install.packages("bigmemory") v4.5.36

All installations take under 5 minutes


Expected run time for complete analysis is 48-72hr 

Expected outcomes are provided in the related html files of the same name

Raw can be found at ENA PRJEB41744 https://www.ebi.ac.uk/ena/browser/view/PRJEB41744 or by contacting authors.  
