Add new training for scATAC-seq batch correction using SnapATAC2

faqs/galaxy/histories_datasets_vs_collections.md

@@ -25,7 +25,7 @@ There is a number of situations when simple collections are not sufficient to re
 
 **Nested collections**
 
-Probably the most common example of this is pared end data when each sample is represented by two files: one containing forward reads and another containing reverse reads. In Galaxy you can create **nested** collection that reflects the hierarchy of the data. In the case of paired data Galaxy supports **paired** collections.
+Probably the most common example of this is paired end data when each sample is represented by two files: one containing forward reads and another containing reverse reads. In Galaxy you can create **nested** collection that reflects the hierarchy of the data. In the case of paired data Galaxy supports **paired** collections.
 
 ![A paired collection is a container containing individual datasets and preserving their hierarchy]({% link shared/images/paired_collection.svg %})
 

topics/single-cell/tutorials/scatac-batch-correction-snapatac2/data-library.yaml

@@ -0,0 +1,43 @@
+---
+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.12683310' 
+      description: latest
+      items:
+      - url: https://zenodo.org/api/records/12683310/files/colon_multisample_01.gz
+        src: url
+        ext: auto
+        info: https://zenodo.org/records/12683310
+      - url: https://zenodo.org/api/records/12683310/files/colon_multisample_02.gz
+        src: url
+        ext: auto
+        info: https://zenodo.org/records/12683310
+      - url: https://zenodo.org/api/records/12683310/files/colon_multisample_03.gz
+        src: url
+        ext: auto
+        info: https://zenodo.org/records/12683310
+      - url: https://zenodo.org/api/records/12683310/files/colon_multisample_04.gz
+        src: url
+        ext: auto
+        info: https://zenodo.org/records/12683310
+      - url: https://zenodo.org/api/records/12683310/files/colon_multisample_05.gz
+        src: url
+        ext: auto
+        info: https://zenodo.org/records/12683310
+      - url: https://zenodo.org/api/records/12683310/files/gencode.v46.annotation.gtf.gz/
+        src: url
+        ext: auto
+        info: https://zenodo.org/records/12683310
+      - url: https://zenodo.org/api/records/12683310/files/chrom_sizes.txt/
+        src: url
+        ext: auto
+        info: https://zenodo.org/records/12683310

topics/single-cell/tutorials/scatac-batch-correction-snapatac2/faqs/index.md

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

topics/single-cell/tutorials/scatac-batch-correction-snapatac2/tutorial.bib

@@ -0,0 +1,111 @@
+
+# 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{Batut2018,
+  doi = {10.1016/j.cels.2018.05.012},
+  url = {https://doi.org/10.1016/j.cels.2018.05.012},
+  year = {2018},
+  month = jun,
+  publisher = {Elsevier {BV}},
+  volume = {6},
+  number = {6},
+  pages = {752--758.e1},
+  author = {B{\'{e}}r{\'{e}}nice Batut and Saskia Hiltemann and Andrea Bagnacani and Dannon Baker and Vivek Bhardwaj and
+           Clemens Blank and Anthony Bretaudeau and Loraine Brillet-Gu{\'{e}}guen and Martin {\v{C}}ech and John Chilton
+           and Dave Clements and Olivia Doppelt-Azeroual and Anika Erxleben and Mallory Ann Freeberg and Simon Gladman and
+           Youri Hoogstrate and Hans-Rudolf Hotz and Torsten Houwaart and Pratik Jagtap and Delphine Larivi{\`{e}}re and
+           Gildas Le Corguill{\'{e}} and Thomas Manke and Fabien Mareuil and Fidel Ram{\'{i}}rez and Devon Ryan and
+           Florian Christoph Sigloch and Nicola Soranzo and Joachim Wolff and Pavankumar Videm and Markus Wolfien and
+           Aisanjiang Wubuli and Dilmurat Yusuf and James Taylor and Rolf Backofen and Anton Nekrutenko and Bj\"{o}rn Gr\"{u}ning},
+  title = {Community-Driven Data Analysis Training for Biology},
+  journal = {Cell Systems}
+}
+@article{Korsunsky2019,
+  title = {Fast,  sensitive and accurate integration of single-cell data with Harmony},
+  volume = {16},
+  ISSN = {1548-7105},
+  url = {http://dx.doi.org/10.1038/s41592-019-0619-0},
+  DOI = {10.1038/s41592-019-0619-0},
+  number = {12},
+  journal = {Nature Methods},
+  publisher = {Springer Science and Business Media LLC},
+  author = {Korsunsky,  Ilya and Millard,  Nghia and Fan,  Jean and Slowikowski,  Kamil and Zhang,  Fan and Wei,  Kevin and Baglaenko,  Yuriy and Brenner,  Michael and Loh,  Po-ru and Raychaudhuri,  Soumya},
+  year = {2019},
+  month = nov,
+  pages = {1289–1296}
+}
+@article{Hie2019,
+  title = {Efficient integration of heterogeneous single-cell transcriptomes using Scanorama},
+  volume = {37},
+  ISSN = {1546-1696},
+  url = {http://dx.doi.org/10.1038/s41587-019-0113-3},
+  DOI = {10.1038/s41587-019-0113-3},
+  number = {6},
+  journal = {Nature Biotechnology},
+  publisher = {Springer Science and Business Media LLC},
+  author = {Hie,  Brian and Bryson,  Bryan and Berger,  Bonnie},
+  year = {2019},
+  month = may,
+  pages = {685–691}
+}
+@article{Haghverdi2018,
+  title = {Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors},
+  volume = {36},
+  ISSN = {1546-1696},
+  url = {http://dx.doi.org/10.1038/nbt.4091},
+  DOI = {10.1038/nbt.4091},
+  number = {5},
+  journal = {Nature Biotechnology},
+  publisher = {Springer Science and Business Media LLC},
+  author = {Haghverdi,  Laleh and Lun,  Aaron T L and Morgan,  Michael D and Marioni,  John C},
+  year = {2018},
+  month = apr,
+  pages = {421–427}
+}
+@article{Luecken2021,
+  title = {Benchmarking atlas-level data integration in single-cell genomics},
+  volume = {19},
+  ISSN = {1548-7105},
+  url = {http://dx.doi.org/10.1038/s41592-021-01336-8},
+  DOI = {10.1038/s41592-021-01336-8},
+  number = {1},
+  journal = {Nature Methods},
+  publisher = {Springer Science and Business Media LLC},
+  author = {Luecken,  Malte D. and B\"{u}ttner,  M. and Chaichoompu,  K. and Danese,  A. and Interlandi,  M. and Mueller,  M. F. and Strobl,  D. C. and Zappia,  L. and Dugas,  M. and Colomé-Tatché,  M. and Theis,  Fabian J.},
+  year = {2021},
+  month = dec,
+  pages = {41–50}
+}
+@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}
+}
+@online{gtn-website,
+  author = {GTN community},
+  title = {GTN Training Materials: Collection of tutorials developed and maintained by the worldwide Galaxy community},
+  url = {https://training.galaxyproject.org},
+  urldate = {2021-03-24}
+}