Sc-candida paper

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).

To clone repository and get the data

You need to install datalad

conda create -n datalad-osf python=3.6
conda activate datalad-osf
conda install -c conda-forge datalad or pip install datalad-osf

Afterwards, configure DataLad to load the datalad-next extension:

git config --global --add datalad.extensions.load next

You then can clone the repository and get the data from osf

datalad clone https://github.com/vdumeaux/sc-candida_paper.git
cd sc-candida_paper

To get all the data (instead of symlinks)

datalad get .

To run the code

Software

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)

scvi environment

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