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.
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The Makefile for read alignment and counting can be found in Mapping.
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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.
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Normalisation contains scripts to normalise scRNAseq data using the BASiCS package.
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The Differential_testing repository holds scripts that perform differential expression and differential variability testing of scRNAseq data.
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All scripts to reproduce the main and supplementary figures can be found in Analysis
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Raw and normalised transcript counts as well as some metadata information are available in Data