Merge pull request #5467 from subinamehta/neoantigen

GTN-tutorials-for-neoantigen

CONTRIBUTORS.yaml

@@ -2130,6 +2130,11 @@ r1corre:
     orcid: 0000-0001-6354-2278
     joined: 2019-04
 
+reid-wagner:
+    name: Reid Wagner
+    email: [email protected] 
+    joined: 2024-11
+
 rikeshi:
     name: Erik Schill
     joined: 2021-05

topics/proteomics/README.md

@@ -19,11 +19,20 @@ topic | features
 [metaQuantome-Taxonomy](tutorials/metaquantome-taxonomy/tutorial.md) | [:book:](tutorials/metaquantome-taxonomy/tutorial.md)
 [metaQuantome-Function](tutorials/metaquantome-function/tutorial.md) | [:book:](tutorials/metaquantome-function/tutorial.md)
 [EncyclopeDIA](tutorials/encyclopedia/tutorial.md) | [:book:](tutorials/encyclopedia/tutorial.md)
+[Neoantigen-1-Fusion-Database-generation](tutorials/neoantigen-1-fusion-database-generation/tutorial.md) | [:book:](tutorials/neoantigen-1-fusion-database-generation/tutorial.md)
+[Neoantigen-2-Non-Normal-Database-generation](tutorials/neoantigen-2-non-normal-database-generation/tutorial.md) | [:book:](tutorials/neoantigen-2-non-normal-database-generation/tutorial.md)
+[Neoantigen-3-Discovery-Peptidomics](tutorials/neoantigen-3-fragpipe-discovery/tutorial.md) | [:book:](tutorials/neoantigen-3-fragpipe-discovery/tutorial.md)
+[Neoantigen-4-Peptidomics-verification](tutorials/neoantigen-4-peptide-verification/tutorial.md) | [:book:](tutorials/neoantigen-4-peptide-verification/tutorial.md)
+[Neoantigen-5-Annotation-and-characterization](tutorials/neoantigen-5-variant-annotation/tutorial.md) | [:book:](tutorials/neoantigen-5-variant-annotation/tutorial.md)
+[Neoantigen-6-HLA-Binding-Prediction](tutorials/neoantigen-6-predicting-hla-binding/tutorial.md) | [:book:](tutorials/neoantigen-6-predicting-hla-binding/tutorial.md)
+[Neoantigen-7-Novel-neoantigen-HLA-Binders](tutorials/neoantigen-7-hla-binding-novel-peptides/tutorial.md) | [:book:](tutorials/neoantigen-7-hla-binding-novel-peptides/tutorial.md)
 [Clinical-Metaproteomics-Database-generation](tutorials/clinical-mp-1-database-generation/tutorial.md) | [:book:](tutorials/clinical-mp-1-database-generation/tutorial.md)
 [Clinical-Metaproteomics-Discovery](tutorials/clinical-mp-2-discovery/tutorial.md) | [:book:](tutorials/clinical-mp-2-discovery/tutorial.md)
 [Clinical-Metaproteomics-Data-Verification](tutorials/clinical-mp-3-verification/tutorial.md) | [:book:](tutorials/clinical-mp-3-verification/tutorial.md)
 [Clinical-Metaproteomics-Quantitation](tutorials/clinical-mp-4-quantitation/tutorial.md) | [:book:](tutorials/clinical-mp-4-quantitation/tutorial.md)
 [Clinical-Metaproteomics-Data-Interpretation](tutorials/clinical-mp-5-data-interpretation/tutorial.md) | [:book:](tutorials/clinical-mp-5-data-interpretation/tutorial.md)
+[Clinical-Metaproteomics-Database-generation](tutorials/clinical-mp-1-database-generation/tutorial.md) | [:book:](tutorials/clinical-mp-1-database-generation/tutorial.md)
+[Clinical-Metaproteomics-Discovery](tutorials/clinical-mp-2-discovery/tutorial.md) | [:book:](tutorials/clinical-mp-2-discovery/tutorial.md)
 [N-Tails](./tutorials/ntails/workflows/) | [:page_facing_up:](https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/ntails/workflows) [:book:](https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/ntails/workflows)
 [Secretome Prediction](https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/secretome-prediction/workflows) | [:page_facing_up:](https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/secretome-prediction/workflows) [:book:](https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/secretome-prediction/workflows)
 

topics/proteomics/metadata.yaml

@@ -40,6 +40,10 @@ subtopics:
   - id: clinical-metaproteomics
     title: "Metaproteomics analysis of clinical data"
     description: "These tutorials are step by step analysis from database generation to the discovery of peptides to verification, quantitation, and interpretation of the results."
+  - id: neoantigen
+    title: "Prediction of potential neoantigens"
+    description: "These tutorials outline the identification, prediction, and validation of potential neoantigens."
+
 references:
   -
     authors: "Kumar D, Yadav AK and Dash D"

topics/proteomics/tutorials/neoantigen-1-fusion-database-generation/faqs/index.md

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

topics/proteomics/tutorials/neoantigen-1-fusion-database-generation/tutorial.bib

@@ -0,0 +1,42 @@
+
+# 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},
+  urldate = {2021-03-24}
+}