flyfl1992/10x

Analyzing 10X Genomics PBMC data

10x genomics 2,700 PBMC GO term exploration

This repository...

Contents

• go_prep.R prepares an expanded GO term library with ancestor GO terms populated for each child term.

• 10x_PBMC_addingGOterms.R loads data into CellRangerR and subsets by a specified GO term.

• 10x_PBMC_dataAnalysis_Seurat.R and 10x_PBMC_dataAnalysis_CellRangerR.R reflect example scripts from tutorials for Seurat and CellRangerR packages, respectively. They are not to be run.

• GO_Search.R will return a vector of ENSEMBL IDs associated with a GO term. This function is now included in 10x_PBMC_addingGOterms.R.

Getting set up

Obtaining the respository

Download or clone the repsoitory from https://github.com/zrlewis/10x

Installing dependencies

Install the following dependencies:

• CellrangerR, follow the installation instructions at https://support.10xgenomics.com/single-cell/software/pipelines/latest/rkit . Tested with version 1.1.0.
• seurat, run the following in R: devtools::install_url("https://github.com/satijalab/seurat/releases/download/v1.4.0/Seurat_1.4.0.9.tgz", binary = TRUE)

Obtaining the data

Data were obtained from https://support.10xgenomics.com/single-cell/software/pipelines/latest/rkit

Before running analyses, you will need to generate a local gene ontology map by running go_prep.R.

Running the analyses

Each time you want to execute an analysis:

• cd to the root of the repository, eg cd 10x
• Run the code, eg lanch R and run source("10x_PBMC_addingGOterms.R")