Merge pull request #4367 from MarisaJL/main

Adding tutorial on trajectory analysis

topics/single-cell/tutorials/scrna-case_trajectories/data-library.yaml

@@ -0,0 +1,20 @@
+---
+destination:
+  type: library
+  name: GTN - Material
+  description: Galaxy Training Network Material
+  synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org
+items:
+- name: Single Cell
+  description: Training material and practicals for all kinds of single cell analysis
+    (particularly scRNA-seq!). When you generate your lovely gene lists for your cells,
+    consider checking out our Transcriptomics tutorials for further network analysis!
+  items:
+  - name: Inferring Trajectories using Scanpy
+    items:
+    - name: 'DOI: 10.5281/zenodo.7075718'
+      description: latest
+      items:
+      - url: https://zenodo.org/api/files/4d8b712c-a2d3-4d91-9235-83a913f87936/Final_cell_annotated_object.h5ad
+        src: url
+        ext: h5ad

topics/single-cell/tutorials/scrna-case_trajectories/tutorial.bib

@@ -0,0 +1,90 @@
+@article {Moreno2020.04.08.032698,
+	author = {Moreno, P. and Huang, N. and Manning, J.R. and Mohammed, S. and Solovyev, A. and Polanski, K. and Chazarra, R. and Talavera-Lopez, C. and Doyle, M. and Marnier, G. and Gr{\"u}ning, B. and Rasche, H. and Bacon, W. and Perez-Riverol, Y. and Haeussler, M. and Meyer, K.B. and Teichmann, S. and Papatheodorou, I.},
+	title = {User-friendly, scalable tools and workflows for single-cell analysis},
+	elocation-id = {2020.04.08.032698},
+	year = {2020},
+	doi = {10.1101/2020.04.08.032698},
+	publisher = {Cold Spring Harbor Laboratory},
+	abstract = {Single-cell RNA-Seq (scRNA-Seq) data analysis requires expertise in command-line tools, programming languages and scaling on compute infrastructure. As scRNA-Seq becomes widespread, computational pipelines need to be more accessible, simpler and scalable. We introduce an interactive analysis environment for scRNA-Seq, based on Galaxy, with ~70 functions from major single-cell analysis tools, which can be run on compute clusters, cloud providers or single machines, to bring compute to the data in scRNA-Seq.Competing Interest StatementThe authors have declared no competing interest.},
+	URL = {https://www.biorxiv.org/content/early/2020/04/09/2020.04.08.032698},
+	eprint = {https://www.biorxiv.org/content/early/2020/04/09/2020.04.08.032698.full.pdf},
+	journal = {bioRxiv}
+}
+
+@article{Bacon2018,
+  doi = {10.3389/fimmu.2018.02523},
+  url = {https://doi.org/10.3389/fimmu.2018.02523},
+  year = {2018},
+  month = nov,
+  publisher = {Frontiers Media {SA}},
+  volume = {9},
+  author = {Wendi A. Bacon and Russell S. Hamilton and Ziyi Yu and Jens Kieckbusch and Delia Hawkes and Ada M. Krzak and Chris Abell and Francesco Colucci and D. Stephen Charnock-Jones},
+  title = {Single-Cell Analysis Identifies Thymic Maturation Delay in Growth-Restricted Neonatal Mice},
+  journal = {Frontiers in Immunology}
+}
+
+@article{Satija2015,
+  doi = {10.1038/nbt.3192},
+  url = {https://doi.org/10.1038/nbt.3192},
+  year = {2015},
+  month = apr,
+  publisher = {Springer Science and Business Media {LLC}},
+  volume = {33},
+  number = {5},
+  pages = {495--502},
+  author = {Rahul Satija and Jeffrey A Farrell and David Gennert and Alexander F Schier and Aviv Regev},
+  title = {Spatial reconstruction of single-cell gene expression data},
+  journal = {Nature Biotechnology}
+}
+
+@article{Wolf2018,
+  doi = {10.1186/s13059-017-1382-0},
+  url = {https://doi.org/10.1186/s13059-017-1382-0},
+  year = {2018},
+  month = feb,
+  publisher = {Springer Science and Business Media {LLC}},
+  volume = {19},
+  number = {1},
+  author = {F. Alexander Wolf and Philipp Angerer and Fabian J. Theis},
+  title = {{SCANPY}: large-scale single-cell gene expression data analysis},
+  journal = {Genome Biology}
+}
+
+@article{Trapnell2014,
+  doi = {10.1038/nbt.2859},
+  url = {https://doi.org/10.1038/nbt.2859},
+  year = {2014},
+  month = mar,
+  publisher = {Springer Science and Business Media {LLC}},
+  volume = {32},
+  number = {4},
+  pages = {381--386},
+  author = {Cole Trapnell and Davide Cacchiarelli and Jonna Grimsby and Prapti Pokharel and Shuqiang Li and Michael Morse and Niall J Lennon and Kenneth J Livak and Tarjei S Mikkelsen and John L Rinn},
+  title = {The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells},
+  journal = {Nature Biotechnology}
+}
+
+@article{McCarthy2017,
+  doi = {10.1093/bioinformatics/btw777},
+  url = {https://doi.org/10.1093/bioinformatics/btw777},
+  year = {2017},
+  month = jan,
+  publisher = {Oxford University Press ({OUP})},
+  pages = {btw777},
+  author = {Davis J. McCarthy and Kieran R. Campbell and Aaron T. L. Lun and Quin F. Wills},
+  title = {Scater: pre-processing,  quality control,  normalization and visualization of single-cell {RNA}-seq data in R},
+  journal = {Bioinformatics}
+}
+
+@article{Cakir2020,
+  doi = {10.1093/nargab/lqaa052},
+  url = {https://doi.org/10.1093/nargab/lqaa052},
+  year = {2020},
+  month = jul,
+  publisher = {Oxford University Press ({OUP})},
+  volume = {2},
+  number = {3},
+  author = {Batuhan Cakir and Martin Prete and Ni Huang and Stijn van~Dongen and Pinar Pir and Vladimir~Yu Kiselev},
+  title = {Comparison of visualization tools for single-cell {RNAseq} data},
+  journal = {{NAR} Genomics and Bioinformatics}
+}