Pan-GI integration

Integration of single cell datasets across the gastrointestinal tract.

Core datasets (remapped using STAR v2.7.9a, human reference Cell Ranger 2020-A using STARsolo pipeline v1.0):

• Williams et al., Cell, 2021, DOI
• Caetano et al., eLife, 2021, DOI
• Huang et al., Cell, 2019, DOI
• Jaeger et al., Nat. Comm., 2021, DOI
• Elmentaite et al., Dev. Cell, 2020, DOI
• Wang et al., J Exp Med, 2020; DOI
• Kinchen et al., Cell, 2018, DOI
• Parikh et al., Nature, 2019, DOI
• James et al., Nat. Immunol., 2020, DOI
• Lee et al., Nature Genetics, 2020, DOI
• Uzzan et al., Nat Med, 2022, DOI
• Che et al., Cell Discov., 2021, DOI
• Domínguez Conde et al., Science, 2022, DOI
• Elmentaite et al., Nature, 2021, DOI
• Holloway et al., Cell Stem Cell, 2020, DOI
• Yu et al., Cell, 2021, DOI
• Li et al., Nat Immunol., 2019, DOI
• Martin et al., Cell, 2019 DOI
• He et al., Genome Biol., 2020 DOI
• Jeong et al., Clin. Cancer Res., 2021 DOI
• Kim et al., NPJ Precis. Oncol., 2022 DOI
• Madisoon et al., Genome Biol., 2019 DOI
• Pagella et al., iScience, 2021 DOI
• Chen et al., J. Dent. Res., 2022 DOI
• Costa-da-Silva et al., iScience, 2022 DOI

Extended atlas (original count matrices used):

• Smillie et al., Cell, 2019, DOI
• Kong et al., Immunity, 2023, DOI
• Garrido-Trigo et al., Nat Comms, 2023 DOI

Contents

• notebooks: this folder contains all notebooks
• scripts: this folder contains scripts