Capturing hidden regulation based on noise change of gene expression level from single cell RNA-seq in yeast
Authors/Creators
- 1. Department of Biology, Faculty of Science, Tohoku University
- 2. Graduate School of Life Sciences, Tohoku University
Description
CreateBASiCS.R
Create BASiCS chain objects, which include mean and noise data, from the raw count matrix. This step takes 10~20 hours.
Main.R
Generate figures in the main results. FunctionSetting.R, DifferenceTestAll.R and DifferenceTestClustest.R are executed in this script.
STP12_detail_analysis.Rmd
Output results mentioned in the discussion. Code is placed within the chunk.
Please make sure to execute this after Main.R .
SupFig1Generator.R
Generate supplement figure 1
YeastGeneNameList.csv
Data that convert ORF id to the common name
This data includes 3 columns, Name, ORF, and SGD.
- Name: Common name (e.g., TSC3)
- ORF: ORF id with Yeastract format (e.g., YBR058C.A)
- SGD: ORF id with SGD format (e.g., YBR058C-A)
GeneticInteraction(ORF).csv
Genetic interaction data downloaded from Yeastract. This data includes two-column, V1 and V2.
The interaction is described as two matrices such as V1 output to V2.
NoiseChangeGeneList
This folder contains data required for generating tables 1 and S2.