doumazane / molecular-atlas

This repository contains the code used for the paper "Molecular Atlas of the Adult Mouse Brain".

A Molecular Atlas of the Adult Mouse Brain

This repository contains the code from the Science Advances paper A Molecular Atlas of the Adult Mouse Brain.
Further information is available at molecularatlas.org, including data to download.

Disclaimer

This code is shared for reproducibility purposes. Despite our efforts, some hardcoded paths and poorly commented parts could be remaining. You might need to modify the code to make it work on your system. The sessionInfo() output is available in the bin directory and will provide guidance about the conditions in which scripts were originally run.

License

This code is shared under the MIT License Agreement. See the LICENSE file for more details.

Authors

Cantin Ortiz [email protected]
Jose Fernandez Navarro [email protected]

Content

Directories 01-registration, 02-qc_normalization, 03-clustering and 04-DEA correspond to the analysis pipeline and are supposed to be executed sequentially.
Directories bin and figures contain the code used to render the figures from intermediary data files.
All data files are available at www.molecularatlas.org.

01-Registration

This script will generate a meta table and a raw count expression table (this will take several hours). Simply cd to the data directory (download) and run the script.

02-qc_normalization

These scripts perform the normalization and batch correction of the expression matrix generated during registration.

03-clustering

This script performs the clustering based on the normalized expression matrix generated previously (download).

04-DEA

These scripts can be run to perform a Differential Expression Analysis (DEA).

05-SC

These scripts can be run to normalize the SC dataset and perform a correlation analysis with the ST dataset.

06-enrichment

This script can be run to perform an enrichment analysis on the gene palette (or any set of genes) and generate some useful plots.

Figures

Figures were generated using many intermediary data files (download). In order to render the figures, you must also download the bin directory and update the two first lines of the script ‘includes.R’:

• path.bin (string): the absolute path to the bin directory
• path.matrices (string): the absolute path to the figures data folder (unzipped)

Before executing a figure script, make sure to run 'includes.R' from the bin. It will load many functions required for plotting.