asd_multiomics_analyses
This repository contains all of the analysis notebooks and scripts used to analyze the ASD multiomics meta-analysis in this paper.
This repository does not contain the datasets required to reproduce the analyses (it amounts to several TB, plus much of the data is confidential). But we have provided the exact directory structure and conda environments used to facilitate the preprocessing and analysis.
Installation
To install the woltka processing utilities, run
conda create env -f woltka.yml
To install the analysis processing utilities, run
conda create env -f analysis.yml
We strongly recommend keeping these two environments separate, since there could dependency issues otherwise.
Preprocessing pipeline
The 16S metadata preprocessing and workflows can be found under the sfari/data/sra folder.
The SMS workflows can be found under the sfari/data/sra_shotgun folder.
The RNAseq preprocessing workflows can be found under the sfari/data/recount3 folder.
Jupyter notebooks
The notebooks are labeled according to the figure numbering in the main paper.