MaAslin2-Tutorial

CONTRIBUTORS.yaml

@@ -1858,7 +1858,11 @@ r1corre:
     twitter: r1corre
     orcid: 0000-0001-6354-2278
     joined: 2019-04
-
+
+renu-pal:
+    name: Renu Pal
+    joined: 2024-07
+
 rikeshi:
     name: Erik Schill
     joined: 2021-05

topics/microbiome/tutorials/multivariable-association/data-library.yaml

@@ -0,0 +1,24 @@
+---
+destination:
+  type: library
+  name: GTN - Material
+  description: Galaxy Training Network Material
+  synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org
+items:
+- name: Microbiome
+  description: Microbiome research has grown substantially over the past decade in terms of the range of biomes sampled, identified taxa, and the volume of data derived from the samples
+  items:
+  - name: Determining multivariable association between various meta’omic features
+      using MaAslin2l
+    items:
+    - name: 'DOI: 10.5281/zenodo.12614561'
+      description: latest
+      items:
+      - url: https://zenodo.org/api/records/12614561/files/HMP2_metadata.tsv/content
+        src: url
+        ext: tabular
+        info: https://zenodo.org/records/12614561
+      - url: https://zenodo.org/api/records/12614561/files/HMP2_taxonomy.tsv
+        src: url
+        ext: tabular
+        info: https://zenodo.org/records/12614561

topics/microbiome/tutorials/multivariable-association/faqs/index.md

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

topics/microbiome/tutorials/multivariable-association/tutorial.bib

@@ -0,0 +1,125 @@
+
+# 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}
+}
+
+@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},
+  note = "[Online; accessed Fri Nov 05 2021]"
+}
+
+@article{Himel2021,
+    title = {Multivariable association discovery in population-scale meta-omics studies},
+    author = {Himel Mallick and Ali Rahnavard and Lauren J. McIver and Siyuan Ma and Yancong Zhang and Long H. Nguyen and Timothy L. Tickle and 
+    	      George Weingart and Boyu Ren and Emma H. Schwager and Suvo Chatterjee and Kelsey N. Thompson and Jeremy E. Wilkinson and 
+    	      Ayshwarya Subramanian and Yiren Lu and Levi Waldron and Joseph N. Paulson and Eric A. Franzosa and Hector Corrada Bravo and 
+    	      Curtis Huttenhower},
+    year = {2021},
+    month = {11},
+    doi={https://doi.org/10.1371/journal.pcbi.1009442},
+    journal = {PLOS COMPUTATIONAL BIOLOGY},    
+    url={https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009442#sec002}
+}
+
+@article{Yang2023,
+    author = {Yang, Lu and Chen, Jun},
+    title = {Benchmarking differential abundance analysis methods for correlated microbiome sequencing data},
+    journal = {Briefings in Bioinformatics},
+    volume = {24},
+    number = {1},
+    pages = {bbac607},
+    year = {2023},
+    month = {01},
+    issn = {1477-4054},
+    doi = {10.1093/bib/bbac607},
+    url = {https://pubmed.ncbi.nlm.nih.gov/36617187/}   
+}
+
+
+@article{Yez2021,
+  title = {Integrating Dietary Data into Microbiome Studies: A Step Forward for Nutri-Metaomics},
+  volume = {13},
+  ISSN = {2072-6643},
+  url = {http://dx.doi.org/10.3390/nu13092978},
+  DOI = {10.3390/nu13092978},
+  number = {9},
+  journal = {Nutrients},
+  publisher = {MDPI AG},
+  author = {Yáñez,  Francisca and Soler,  Zaida and Oliero,  Manon and Xie,  Zixuan and Oyarzun,  Iñigo and Serrano-Gómez,  Gerard 
+  	   and Manichanh,  Chaysavanh},
+  year = {2021},
+  month = {08},
+  pages = {2978}
+}
+
+@article{Reasoner2024,
+  title = {Longitudinal profiling of the intestinal microbiome in children with cystic fibrosis treated with elexacaftor-tezacaftor-ivacaftor},
+  volume = {15},
+  ISSN = {2150-7511},
+  url = {http://dx.doi.org/10.1128/mbio.01935-23},
+  DOI = {10.1128/mbio.01935-23},
+  number = {2},
+  journal = {mBio},
+  publisher = {American Society for Microbiology},
+  author = {Reasoner,  Seth A. and Bernard,  Rachel and Waalkes,  Adam and Penewit,  Kelsi and Lewis,  Janessa and Sokolow,  Andrew G. and Brown, 
+  	    Rebekah F. and Edwards,  Kathryn M. and Salipante,  Stephen J. and Hadjifrangiskou,  Maria and Nicholson,  Maribeth R.},
+  editor = {Pier,  Gerald B. and O’Toole,  George},
+  year = {2024},
+  month = {02} 
+}
+
+@article{Lebeaux2021,
+  title = {The infant gut resistome is associated with E. coli and early-life exposures},
+  volume = {21},
+  ISSN = {1471-2180},
+  url = {http://dx.doi.org/10.1186/s12866-021-02129-x},
+  DOI = {10.1186/s12866-021-02129-x},
+  number = {1},
+  journal = {BMC Microbiology},
+  publisher = {Springer Science and Business Media LLC},
+  author = {Lebeaux,  Rebecca M. and Coker,  Modupe O. and Dade,  Erika F. and Palys,  Thomas J. and Morrison,  Hilary G. and Ross,  
+  	   Benjamin D. and Baker,  Emily R. and Karagas,  Margaret R. and Madan,  Juliette C. and Hoen,  Anne G.},
+  year = {2021},
+  month = {07}
+}
+
+@misc{IBDMDB,
+  author = {IBD MDB Consortium},
+  title = {The Inflammatory Bowel Disease Multi-omics Database},
+  url = {https://ibdmdb.org/},
+  note = "[Online; accessed 2021-03-24]"
+}
+