This is the code and data associated with our study published in eLife in 2023.
Please cite: Dumeaux V, Massahi S, Bettauer V, Khurdia S, Costa ACBP, Omran RP, Simpson S, Xie JL, Whiteway M, Berman J, Hallett MT. Candida albicans exhibits adaptive cytoprotective responses to anti-fungal compounds. Elife 2023;12:e81406 https://dx.doi.org/10.7554/eLife.81406
We use OSF as a special remote to store data in the annex of this repository : we published the repository to GitHub and have the data published to the OSF (via a publication dependency).
You need to install datalad
conda create -n datalad-osf -c conda-forge datalad python=3.6
conda activate datalad-osf
You then can clone the repository and get the data from osf
git clone https://github.com/vdumeaux/sc-candida_paper.git
cd sc-candida_paper
datalad get .
You need to have the following software installed and change the paths in src/init.R
:
- sra-toolkit
- Salmon 1.6.0
- alevin-fry 0.4.3 (bioconda)
- STAR 2.7.9a
- dropEst 0.8.6
- TrimGalore 0.6.6
- cutadapt 1.18 (bioconda)
To run scvi notebook, create a new scvi-env as follow:
conda create --name scvi-env scvi-tools rpy2=3.4.2 scanpy anndata2ri anndata bioconductor-singlecellexperiment leidenalg phate gprofiler-official scprep graphtools meld -c bioconda -c conda-forge
pip install --user magic-impute
OR
conda env create -f scvi-env.yml