Add new training for scATAC-seq analysis using SnapATAC2

CONTRIBUTORS.yaml

@@ -2067,6 +2067,10 @@ thomaswollmann:
       - deNBI
       - elixir-europe
 
+timonschlegel:
+    name: Timon Schlegel
+    joined: 2024-05
+
 timothygriffin:
     name: Timothy J. Griffin
     email: [email protected]

topics/single-cell/faqs/single_cell_omics.md

@@ -1,15 +1,15 @@
 ---
-title: Use our Single Cell Lab
+title: Use our Single Cell Omics Lab
 area: Resources
 box_type: tip
 layout: faq
 contributors: [nomadscientist]
 ---
 
-Did you know we have a unique Single Cell Lab with all our single cell tools highlighted to make it easier to use on Galaxy? We recommend this site for all your single cell analysis needs, particularly for newer users.
+Did you know we have a unique Single Cell Omics Lab with all our single cell tools highlighted to make it easier to use on Galaxy? We recommend this site for all your single cell analysis needs, particularly for newer users.
 
-The Single Cell Lab currently uses the main European Galaxy infrastructure and power, it's just organised better for users of particular analyses...like single cell!
+The Single Cell Omics Lab currently uses the main European Galaxy infrastructure and power, it's just organised better for users of particular analyses...like single cell!
 
 Try it out! All your histories/workflows/logins from the general [European Galaxy server](https://usegalaxy.eu) will be there!
 
- - {% icon subdomain %} [Single Cell Lab](https://singlecell.usegalaxy.eu)
+ - {% icon subdomain %} [Single Cell Omics Lab](https://singlecell.usegalaxy.eu)

topics/single-cell/tutorials/scatac-preprocessing-tenx/tutorial.md

@@ -35,6 +35,7 @@ follow_up_training:
     topic_name: single-cell
     tutorials:
       - scrna-scanpy-pbmc3k
+      - scatac-standard-processing-snapatac2
 
 contributors:
   - pavanvidem

topics/single-cell/tutorials/scatac-standard-processing-snapatac2/data-library.yaml

@@ -0,0 +1,31 @@
+---
+destination:
+  type: library
+  name: GTN - Material
+  description: Galaxy Training Network Material
+  synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org
+items:
+- name: The new topic
+  description: Summary
+  items:
+  - name: scATAC-seq standard processing with SnapATAC2
+    items:
+    - name: 'DOI: 10.5281/zenodo.11473531' 
+      description: latest
+      items:
+      - url: https://zenodo.org/api/records/11473531/files/atac_pbmc_5k_nextgem_fragments.tsv/
+        src: url
+        ext: auto
+        info: https://zenodo.org/records/11473531
+      - url: https://zenodo.org/api/records/11473531/files/gencode.v46.annotation.gtf.gz/
+        src: url
+        ext: auto
+        info: https://zenodo.org/records/11473531
+      - url: https://zenodo.org/api/records/11473531/files/chrom_sizes.txt/
+        src: url
+        ext: auto
+        info: https://zenodo.org/records/11473531
+      - url: https://zenodo.org/api/records/11473531/files/BAM_500-PBMC.bam/
+        src: url
+        ext: auto
+        info: https://zenodo.org/records/11473531

topics/single-cell/tutorials/scatac-standard-processing-snapatac2/faqs/index.md

@@ -0,0 +1,3 @@
+---
+layout: faq-page
+---

topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.bib

@@ -0,0 +1,177 @@
+
+# This is the bibliography file for your tutorial.
+#
+# To add bibliography (bibtex) entries here, follow these steps:
+#  1) Find the DOI for the article you want to cite
+#  2) Go to https://doi2bib.org and fill in the DOI
+#  3) Copy the resulting bibtex entry into this file
+#
+# To cite the example below, in your tutorial.md file
+# use {% cite Batut2018 %}
+#
+# If you want to cite an online resourse (website etc)
+# you can use the 'online' format (see below)
+#
+# You can remove the examples below
+@article{Kia2017,
+  title = {Improved genome sequencing using an engineered transposase},
+  volume = {17},
+  ISSN = {1472-6750},
+  url = {http://dx.doi.org/10.1186/s12896-016-0326-1},
+  DOI = {10.1186/s12896-016-0326-1},
+  number = {1},
+  journal = {BMC Biotechnology},
+  publisher = {Springer Science and Business Media LLC},
+  author = {Kia,  Amirali and Gloeckner,  Christian and Osothprarop,  Trina and Gormley,  Niall and Bomati,  Erin and Stephenson,  Michelle and Goryshin,  Igor and He,  Molly Min},
+  year = {2017},
+  month = jan 
+}
+@article{Zhang2024,
+  title = {A fast,  scalable and versatile tool for analysis of single-cell omics data},
+  volume = {21},
+  ISSN = {1548-7105},
+  url = {http://dx.doi.org/10.1038/s41592-023-02139-9},
+  DOI = {10.1038/s41592-023-02139-9},
+  number = {2},
+  journal = {Nature Methods},
+  publisher = {Springer Science and Business Media LLC},
+  author = {Zhang,  Kai and Zemke,  Nathan R. and Armand,  Ethan J. and Ren,  Bing},
+  year = {2024},
+  month = jan,
+  pages = {217–227}
+}
+@article{Traag2019,
+  title = {From Louvain to Leiden: guaranteeing well-connected communities},
+  volume = {9},
+  ISSN = {2045-2322},
+  url = {http://dx.doi.org/10.1038/s41598-019-41695-z},
+  DOI = {10.1038/s41598-019-41695-z},
+  number = {1},
+  journal = {Scientific Reports},
+  publisher = {Springer Science and Business Media LLC},
+  author = {Traag,  V. A. and Waltman,  L. and van Eck,  N. J.},
+  year = {2019},
+  month = mar 
+}
+@misc{McInnes2018,
+  doi = {10.48550/ARXIV.1802.03426},
+  url = {https://arxiv.org/abs/1802.03426},
+  author = {McInnes,  Leland and Healy,  John and Melville,  James},
+  keywords = {Machine Learning (stat.ML),  Computational Geometry (cs.CG),  Machine Learning (cs.LG),  FOS: Computer and information sciences,  FOS: Computer and information sciences},
+  title = {UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction},
+  publisher = {arXiv},
+  year = {2018},
+  copyright = {arXiv.org perpetual,  non-exclusive license}
+}
+@article{Belkin2003,
+  title = {Laplacian Eigenmaps for Dimensionality Reduction and Data Representation},
+  volume = {15},
+  ISSN = {1530-888X},
+  url = {http://dx.doi.org/10.1162/089976603321780317},
+  DOI = {10.1162/089976603321780317},
+  number = {6},
+  journal = {Neural Computation},
+  publisher = {MIT Press - Journals},
+  author = {Belkin,  Mikhail and Niyogi,  Partha},
+  year = {2003},
+  month = jun,
+  pages = {1373–1396}
+}
+@article{Sun2019,
+  title = {A Bayesian mixture model for clustering droplet-based single-cell transcriptomic data from population studies},
+  volume = {10},
+  ISSN = {2041-1723},
+  url = {http://dx.doi.org/10.1038/s41467-019-09639-3},
+  DOI = {10.1038/s41467-019-09639-3},
+  number = {1},
+  journal = {Nature Communications},
+  publisher = {Springer Science and Business Media LLC},
+  author = {Sun,  Zhe and Chen,  Li and Xin,  Hongyi and Jiang,  Yale and Huang,  Qianhui and Cillo,  Anthony R. and Tabib,  Tracy and Kolls,  Jay K. and Bruno,  Tullia C. and Lafyatis,  Robert and Vignali,  Dario A. A. and Chen,  Kong and Ding,  Ying and Hu,  Ming and Chen,  Wei},
+  year = {2019},
+  month = apr 
+}
+@article{Wolf2018,
+  title = {SCANPY: large-scale single-cell gene expression data analysis},
+  volume = {19},
+  ISSN = {1474-760X},
+  url = {http://dx.doi.org/10.1186/s13059-017-1382-0}, 
+  DOI = {10.1186/s13059-017-1382-0},
+  number = {1},
+  journal = {Genome Biology},
+  publisher = {Springer Science and Business Media LLC},
+  author = {Wolf,  F. Alexander and Angerer,  Philipp and Theis,  Fabian J.},
+  year = {2018},
+  month = feb 
+}
+@article{Yan2020,
+  title = {From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis},
+  volume = {21},
+  ISSN = {1474-760X},
+  url = {http://dx.doi.org/10.1186/s13059-020-1929-3},
+  DOI = {10.1186/s13059-020-1929-3},
+  number = {1},
+  journal = {Genome Biology},
+  publisher = {Springer Science and Business Media LLC},
+  author = {Yan,  Feng and Powell,  David R. and Curtis,  David J. and Wong,  Nicholas C.},
+  year = {2020},
+  month = feb 
+}
+@article{Amemiya2019,
+  title = {The ENCODE Blacklist: Identification of Problematic Regions of the Genome},
+  volume = {9},
+  ISSN = {2045-2322},
+  url = {http://dx.doi.org/10.1038/s41598-019-45839-z},
+  DOI = {10.1038/s41598-019-45839-z},
+  number = {1},
+  journal = {Scientific Reports},
+  publisher = {Springer Science and Business Media LLC},
+  author = {Amemiya,  Haley M. and Kundaje,  Anshul and Boyle,  Alan P.},
+  year = {2019},
+  month = jun 
+}
+@article{Franzn2019,
+  title = {PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data},
+  volume = {2019},
+  ISSN = {1758-0463},
+  url = {http://dx.doi.org/10.1093/database/baz046},
+  DOI = {10.1093/database/baz046},
+  journal = {Database},
+  publisher = {Oxford University Press (OUP)},
+  author = {Franzén,  Oscar and Gan,  Li-Ming and Bj\"{o}rkegren,  Johan L M},
+  year = {2019},
+  month = jan 
+}
+@article{Wolock2019,
+  title = {Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data},
+  volume = {8},
+  ISSN = {2405-4712},
+  url = {http://dx.doi.org/10.1016/j.cels.2018.11.005},
+  DOI = {10.1016/j.cels.2018.11.005},
+  number = {4},
+  journal = {Cell Systems},
+  publisher = {Elsevier BV},
+  author = {Wolock,  Samuel L. and Lopez,  Romain and Klein,  Allon M.},
+  year = {2019},
+  month = apr,
+  pages = {281--291.e9}
+}
+@article{vanDijk2018,
+  title = {Recovering Gene Interactions from Single-Cell Data Using Data Diffusion},
+  volume = {174},
+  ISSN = {0092-8674},
+  url = {http://dx.doi.org/10.1016/j.cell.2018.05.061},
+  DOI = {10.1016/j.cell.2018.05.061},
+  number = {3},
+  journal = {Cell},
+  publisher = {Elsevier BV},
+  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 Bierie,  Brian and Mazutis,  Linas and Wolf,  Guy and Krishnaswamy,  Smita and Pe’er,  Dana},
+  year = {2018},
+  month = jul,
+  pages = {716--729.e27}
+}
+@online{snapatac2_docs,
+  author = {Kai Zhang},
+  title = {SnapATAC2: A Python/Rust package for single-cell epigenomics analysis},
+  url = {https://kzhang.org/SnapATAC2/version/2.5/index.html},
+  urldate = {2024-06-03}
+}