biolchen/immuneaging2017

Code for Celia and Nils' immune aging project.

R code used for data analysis of Jimenez-Martinez et al., Science (2017)

The R scripts for read mapping and counting, computational filtering (quality control), normalisation, differential expression analysis and for figure generation can be found in this repository.

• The Makefile for read alignment and counting can be found in Mapping.

• Quality control and filtering of low quality cells/genes is described in Quality_control. This folder contains the scripts to reproduce Fig. S1 and Fig. S2.

• Normalisation contains scripts to normalise scRNAseq data using the BASiCS package.

• The Differential_testing repository holds scripts that perform differential expression and differential variability testing of scRNAseq data.

• All scripts to reproduce the main and supplementary figures can be found in Analysis

• Raw and normalised transcript counts as well as some metadata information are available in Data