/TENxBrainAnalysis

R scripts for analyzing the 1.3 million brain cell data set from 10X Genomics

Primary LanguageR

Scripts for analyzing the 10X 1.3 million brain cell data

The scripts should be executed in the following order:

  • intro.Rmd: An introduction, duh.
  • preprocess.Rmd: Downloading the data and quality control
  • cycle.Rmd: Cell cycle phase assignment
  • normalize.Rmd: Calculation of cell-specific size factors
  • variance.Rmd: Identification of highly variable genes
  • dimred.Rmd: Dimensionality reduction with randomized PCA

Various output objects will be saved to objects/. A few of these objects are currently hosted at https://drive.google.com/open?id=1_0WbmJ2BriLKlyKEf1Bbb8K0_NwD9rw-. Note that sce.rds does not contain the actual counts or normalized expression values, and requires something like this:

library(TENxBrainData)
tenx <- TENxBrainData()
sce <- readRDS("sce.rds")
tenx <- tenx[,colnames(sce)] # drop 19,672 cells from the raw TENxBrainData
counts(sce) <- counts(tenx) # overwrite inbuilt absolute path
library(scater)
sce <- normalize(sce) # generate normalized expression values

The pics/make_pics.R scripts will generate the figures used in the paper.