Merge pull request #5709 from KristinaGomoryova/scp_training

Training for the bioconductor-scp tool

CONTRIBUTORS.yaml

@@ -1401,6 +1401,14 @@ kostrykin:
       - elixir-europe
       - deNBI
 
+KristinaGomoryova:
+    name: Kristina Gomoryova
+    orcid: 0000-0003-4407-3917
+    joined: 2025-01
+    email: gomoryova@sci.muni.cz
+    elixir_node: cz
+    twitter: kristina_gomory
+
 kxk302:
     name: Kaivan Kamali
     email: kxk302@gmail.com

topics/proteomics/tutorials/bioconductor-scp/faqs/index.md

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

topics/proteomics/tutorials/bioconductor-scp/tutorial.bib

@@ -0,0 +1,150 @@
+
+# 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{Lin2024,
+  title = {Review and Practical Guide for Getting Started With Single‐Cell Proteomics},
+  volume = {25},
+  ISSN = {1615-9861},
+  url = {http://dx.doi.org/10.1002/pmic.202400021},
+  DOI = {10.1002/pmic.202400021},
+  number = {1–2},
+  journal = {PROTEOMICS},
+  publisher = {Wiley},
+  author = {Lin,  Hsien‐Jung L. and Webber,  Kei G. I. and Nwosu,  Andikan J. and Kelly,  Ryan T.},
+  year = {2024},
+  month = nov 
+}
+
+@article{Gatto2023,
+  title = {Initial recommendations for performing,  benchmarking and reporting single-cell proteomics experiments},
+  volume = {20},
+  ISSN = {1548-7105},
+  url = {http://dx.doi.org/10.1038/s41592-023-01785-3},
+  DOI = {10.1038/s41592-023-01785-3},
+  number = {3},
+  journal = {Nature Methods},
+  publisher = {Springer Science and Business Media LLC},
+  author = {Gatto,  Laurent and Aebersold,  Ruedi and Cox,  Juergen and Demichev,  Vadim and Derks,  Jason and Emmott,  Edward and Franks,  Alexander M. and Ivanov,  Alexander R. and Kelly,  Ryan T. and Khoury,  Luke and Leduc,  Andrew and MacCoss,  Michael J. and Nemes,  Peter and Perlman,  David H. and Petelski,  Aleksandra A. and Rose,  Christopher M. and Schoof,  Erwin M. and Van Eyk,  Jennifer and Vanderaa,  Christophe and Yates,  John R. and Slavov,  Nikolai},
+  year = {2023},
+  month = mar,
+  pages = {375–386}
+}
+
+@article{Ahmad2023,
+  title = {A review of the current state of single-cell proteomics and future perspective},
+  volume = {415},
+  ISSN = {1618-2650},
+  url = {http://dx.doi.org/10.1007/s00216-023-04759-8},
+  DOI = {10.1007/s00216-023-04759-8},
+  number = {28},
+  journal = {Analytical and Bioanalytical Chemistry},
+  publisher = {Springer Science and Business Media LLC},
+  author = {Ahmad,  Rushdy and Budnik,  Bogdan},
+  year = {2023},
+  month = jun,
+  pages = {6889–6899}
+}
+
+@article{Specht2021,
+  title = {Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2},
+  volume = {22},
+  ISSN = {1474-760X},
+  url = {http://dx.doi.org/10.1186/s13059-021-02267-5},
+  DOI = {10.1186/s13059-021-02267-5},
+  number = {1},
+  journal = {Genome Biology},
+  publisher = {Springer Science and Business Media LLC},
+  author = {Specht,  Harrison and Emmott,  Edward and Petelski,  Aleksandra A. and Huffman,  R. Gray and Perlman,  David H. and Serra,  Marco and Kharchenko,  Peter and Koller,  Antonius and Slavov,  Nikolai},
+  year = {2021},
+  month = jan 
+}
+
+@online{creative-proteomics,
+  author = {Creative Proteomics},
+  title = {Principal Component Analysis},
+  url = {https://www.creative-proteomics.com/services/pca-service.htm},
+  urldate = {2025-01-21}
+}
+
+@article{Phua2022,
+  title = {Perspectives for better batch effect correction in mass-spectrometry-based proteomics},
+  volume = {20},
+  ISSN = {2001-0370},
+  url = {http://dx.doi.org/10.1016/j.csbj.2022.08.022},
+  DOI = {10.1016/j.csbj.2022.08.022},
+  journal = {Computational and Structural Biotechnology Journal},
+  publisher = {Elsevier BV},
+  author = {Phua,  Ser-Xian and Lim,  Kai-Peng and Goh,  Wilson Wen-Bin},
+  year = {2022},
+  pages = {4369–4375}
+}
+
+@article{Zhang2018,
+  title = {Alternative empirical Bayes models for adjusting for batch effects in genomic studies},
+  volume = {19},
+  ISSN = {1471-2105},
+  url = {http://dx.doi.org/10.1186/s12859-018-2263-6},
+  DOI = {10.1186/s12859-018-2263-6},
+  number = {1},
+  journal = {BMC Bioinformatics},
+  publisher = {Springer Science and Business Media LLC},
+  author = {Zhang,  Yuqing and Jenkins,  David F. and Manimaran,  Solaiappan and Johnson,  W. Evan},
+  year = {2018},
+  month = jul 
+}
+
+@online{distill-tSNE,
+  author = {Distill},
+  title = {How to Use t-SNE Effectively},
+  url = {https://distill.pub/2016/misread-tsne/},
+  urldate = {2025-01-21}
+}
+
+@online{understanding-umap,
+  author = {Coenen, Pearce},
+  title = {Understanding UMAP},
+  url = {https://pair-code.github.io/understanding-umap/},
+  urldate = {2025-01-21}
+}
+
+@online{understanding-umap2,
+  author = {Aastha Varma},
+  title = {Dimensionality Reduction: PCA, t-SNE, and UMAP},
+  url = {https://medium.com/@aastha.code/dimensionality-reduction-pca-t-sne-and-umap-41d499da2df2},
+  urldate = {2025-01-21}
+}
+
+@online{number-pca-components,
+  author = {Kevin O'Brien},
+  title = {https://rpubs.com/DragonflyStats/pca_components_number},
+  url = {https://rpubs.com/DragonflyStats/pca_components_number},
+  urldate = {2025-01-21}
+}
+
+@article{Goh2017,
+  title = {Why Batch Effects Matter in Omics Data,  and How to Avoid Them},
+  volume = {35},
+  ISSN = {0167-7799},
+  url = {http://dx.doi.org/10.1016/j.tibtech.2017.02.012},
+  DOI = {10.1016/j.tibtech.2017.02.012},
+  number = {6},
+  journal = {Trends in Biotechnology},
+  publisher = {Elsevier BV},
+  author = {Goh,  Wilson Wen Bin and Wang,  Wei and Wong,  Limsoon},
+  year = {2017},
+  month = jun,
+  pages = {498–507}
+}