README

R Implementation of Sincera: a Computational Pipeline for Single-cell RNA-seq Profiling Analysis

Author: Minzhe Guo (minzhe.guo@cchmc.org)
Version: alpha.03012015
Status: core functions of Sincera are ready; we are working on the documentation, interface, result presentation, and error handling improvement. 

DESCRIPTION OF FILES:

1) E16.5.Rd: R data object file containing Single-cell RNA-seq expression data from mouse lung at E16.5 and gene-celltype association data downloaded from EBI Expression Atlas.
				exprs.m: the FPKM values of 36188 Ensembl genes in 148 cells
				cells: the information of 148 cells, the cluster membership of cells used in the manuscript is encoded in the column "CLUSTER"
				genes: the information of 36188 Ensembl genes
				celltype.gene.association: processed cell type and gene association data downloaded from EBI Expression Atlas (http://www.ebi.ac.uk/gxa/)
				celltype.genome.count: the hits of each cell type in the genome of 36188 Ensembl genes
				data4cm: data for demonstrating the consensus-maximization-based refinement of regulatory target prediction for Nkx2-1 in epithelial cells
2) sincera: R functions to implement the pipeline.
3) demo.R: R functions to utilize Sincera for analysing E16.5 data.

INSTALLATION AND RUNNING THE DEMO

1) Download and unzip the sincera package, sincera.a03012015.zip
2) Open R GUI (required version >= 3.1.2)
3) Change the directory of R GUI to the unzipped directory
4) Run the demo by sourcing demo.R in R GUI.