Merge pull request #37 from quadbio/docs/smoothing_tutorial

Add tutorial on data smoothing

Author: Marius1311

docs/notebooks/tutorials/data_denoising.ipynb

@@ -21,18 +21,6 @@ @article{cao2022multi
   url={https://www.nature.com/articles/s41587-022-01284-4},
 }
 
-@article{van2018recovering,
-  title={Recovering gene interactions from single-cell data using data diffusion},
-  author={Van Dijk, David and Sharma, Roshan and Nainys, Juozas and Yim, Kristina and Kathail, Pooja and Carr, Ambrose J and Burdziak, Cassandra and Moon, Kevin R and Chaffer, Christine L and Pattabiraman, Diwakar and others},
-  journal={Cell},
-  volume={174},
-  number={3},
-  pages={716--729},
-  year={2018},
-  publisher={Elsevier},
-  url={https://www.sciencedirect.com/science/article/pii/S0092867418307244?via%3Dihub},
-}
-
 @article{lotfollahi2022mapping,
   title={Mapping single-cell data to reference atlases by transfer learning},
   author={Lotfollahi, Mohammad and Naghipourfar, Mohsen and Luecken, Malte D and Khajavi, Matin and B{\"u}ttner, Maren and Wagenstetter, Marco and Avsec, {\v{Z}}iga and Gayoso, Adam and Yosef, Nir and Interlandi, Marta and others},
@@ -256,3 +244,63 @@ @article{xia2023spatial
   publisher={Nature Publishing Group UK London},
   url={https://www.nature.com/articles/s41467-023-43105-5},
 }
+
+@article{van2018recovering,
+  title={Recovering gene interactions from single-cell data using data diffusion},
+  author={Van Dijk, David and Sharma, Roshan and Nainys, Juozas and Yim, Kristina and Kathail, Pooja and Carr, Ambrose J and Burdziak, Cassandra and Moon, Kevin R and Chaffer, Christine L and Pattabiraman, Diwakar and others},
+  journal={Cell},
+  volume={174},
+  number={3},
+  pages={716--729},
+  year={2018},
+  publisher={Elsevier},
+  url={https://www.sciencedirect.com/science/article/pii/S0092867418307244?via%3Dihub},
+}
+
+@article{setty2019characterization,
+  title={Characterization of cell fate probabilities in single-cell data with Palantir},
+  author={Setty, Manu and Kiseliovas, Vaidotas and Levine, Jacob and Gayoso, Adam and Mazutis, Linas and Pe’Er, Dana},
+  journal={Nature biotechnology},
+  volume={37},
+  number={4},
+  pages={451--460},
+  year={2019},
+  publisher={Nature Publishing Group US New York},
+  url={https://www.nature.com/articles/s41587-019-0068-4},
+}
+
+@article{bastidas2019comprehensive,
+  title={Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis},
+  author={Bastidas-Ponce, Aim{\'e}e and Tritschler, Sophie and Dony, Leander and Scheibner, Katharina and Tarquis-Medina, Marta and Salinno, Ciro and Schirge, Silvia and Burtscher, Ingo and B{\"o}ttcher, Anika and Theis, Fabian J and others},
+  journal={Development},
+  volume={146},
+  number={12},
+  pages={dev173849},
+  year={2019},
+  publisher={The Company of Biologists Ltd},
+  url={https://journals.biologists.com/dev/article/146/12/dev173849/19483/Comprehensive-single-cell-mRNA-profiling-reveals-a},
+}
+
+@article{lange2022cellrank,
+  title={CellRank for directed single-cell fate mapping},
+  author={Lange, Marius and Bergen, Volker and Klein, Michal and Setty, Manu and Reuter, Bernhard and Bakhti, Mostafa and Lickert, Heiko and Ansari, Meshal and Schniering, Janine and Schiller, Herbert B and others},
+  journal={Nature methods},
+  volume={19},
+  number={2},
+  pages={159--170},
+  year={2022},
+  publisher={Nature Publishing Group US New York},
+  url={https://www.nature.com/articles/s41592-021-01346-6},
+}
+
+@article{weiler2024cellrank,
+  title={CellRank 2: unified fate mapping in multiview single-cell data},
+  author={Weiler, Philipp and Lange, Marius and Klein, Michal and Pe’er, Dana and Theis, Fabian},
+  journal={Nature Methods},
+  volume={21},
+  number={7},
+  pages={1196--1205},
+  year={2024},
+  publisher={Nature Publishing Group US New York},
+  url={https://www.nature.com/articles/s41592-024-02303-9},
+}