biocbook: transfer chaps 60/61 to inst/pages/

DESCRIPTION

@@ -77,6 +77,9 @@ Suggests:
     stringr, 
     ComplexHeatmap, 
     reticulate,
+    igraph, 
+    corpcor, 
+    circlize, 
     BiocBook
 Remotes:
     github::microbiome/miaTime

README.md

@@ -6,7 +6,7 @@
 
 **README from [microbiome/OMA](https://github.com/microbiome/OMA)**
 
-# Orchestrating Microbiome Analysis Book <img src="general/figures/mia_logo.png" align="right" width="120" />
+# Orchestrating Microbiome Analysis Book <img src="images/mia_logo.png" align="right" width="120" />
 
 ## Overview
 

inst/assets/_book.yml

@@ -17,6 +17,8 @@ book:
         - pages/21_microbiome_community.qmd
         - pages/24_clustering.qmd
         - pages/30_differential_abundance.qmd
+        - pages/60_network_learning.qmd
+        - pages/61_network_comparison.qmd
         - pages/40_machine_learning.qmd
         - pages/23_multi-assay_analyses.qmd
         - pages/19_visualization_techniques.qmd

inst/assets/bibliography.bib

@@ -1493,3 +1493,342 @@ @article{Schloss2023
   publisher = {Cold Spring Harbor Laboratory},
   doi = {10.1101/2023.06.23.546313}
 }
+
+@article{schafer2005shrinkage,
+author = {Sch{\"a}fer, Juliane and Strimmer, Korbinian},
+doi = {10.2202/1544-6115.1175},
+journal = {{Statistical Applications in Genetics and Molecular Biology}},
+number = {1},
+pages = {1--30},
+title = {{A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics}},
+volume = {4},
+year = {2005}
+}
+
+
+@article{yoon2019microbial,
+  title = {{Microbial networks in SPRING - Semi-parametric rank-based correlation and partial correlation estimation for quantitative microbiome data}},
+  author = {Yoon, Grace and Gaynanova, Irina and M{\"u}ller, Christian L},
+  journal = {{Frontiers in Genetics}},
+  volume = {10},
+  pages = {516},
+  year = {2019},
+  doi = {10.3389/fgene.2019.00516}
+}
+
+
+@article{yoon2021fast,
+  title={Fast computation of latent correlations},
+  author={Yoon, Grace and M{\"u}ller, Christian L and Gaynanova, Irina},
+  journal={{Journal of Computational and Graphical Statistics}},
+  volume={30},
+  number={4},
+  pages={1249--1256},
+  year={2021}
+}
+
+
+@article{peschel2021netcomi,
+    author = {Peschel, Stefanie and M{\"{u}}ller, Christian L and von Mutius, Erika and Boulesteix, Anne-Laure and Depner, Martin},
+    title = {{NetCoMi: network construction and comparison for microbiome data in R}},
+    journal = {{Briefings in Bioinformatics}},
+    volume = {22},
+    number = {4},
+    pages = {bbaa290},
+    year = {2021},
+    doi = {10.1093/bib/bbaa290}
+}
+
+
+@article{potbhare2022skin,
+  title = {Skin microbiota diversity among genetically unrelated individuals of Indian origin},
+  author = {Potbhare, Renuka and RaviKumar, Ameeta and Munukka, Eveliina and Lahti, Leo and Ashma, Richa},
+  journal = {{PeerJ}},
+  volume = {10},
+  pages = {e13075},
+  year = {2022},
+  doi = {10.7717/peerj.13075}
+}
+
+
+@article{vanDongen2012metric,
+arxivId = {1208.3145},
+author = {van Dongen, Stijn and Enright, Anton J.},
+eprint = {1208.3145},
+pages = {2--6},
+title = {{Metric distances derived from cosine similarity and Pearson and Spearman correlations}},
+url = {http://arxiv.org/abs/1208.3145},
+journal={{arXiv preprint}},
+volume = {2},
+year = {2012}
+}
+
+
+@article{ullmann2023over,
+  title = {Over-optimism in unsupervised microbiome analysis: Insights from network learning and clustering},
+  author = {Ullmann, Theresa and Peschel, Stefanie and Finger, Philipp and M{\"u}ller, Christian L and Boulesteix, Anne-Laure},
+  journal = {{PLoS Computational Biology}},
+  volume = {19},
+  number = {1},
+  pages = {e1010820},
+  year = {2023},
+  doi = {10.1371/journal.pcbi.1010820}
+}
+
+
+@article{meinshausen2006high,
+author = {Meinshausen, Nicolai and B{\"{u}}hlmann, Peter},
+doi = {10.1214/009053606000000281},
+journal = {{Annals of Statistics}},
+number = {3},
+pages = {1436--1462},
+title = {{High-dimensional graphs and variable selection with the Lasso}},
+volume = {34},
+year = {2006}
+}
+
+
+@article{friedman2008sparse,
+author = {Friedman, Jerome and Hastie, Trevor and Tibshirani, Robert},
+doi = {10.1093/BIOSTATISTICS/KXM045},
+issn = {1468-4357},
+journal = {{Biostatistics (Oxford, England)}},
+month = {jul},
+number = {3},
+pages = {432--441},
+publisher = {Biostatistics},
+title = {{Sparse inverse covariance estimation with the graphical lasso}},
+volume = {9},
+year = {2008}
+}
+
+
+@article{lovell2015proportionality,
+author = {Lovell, David and Pawlowsky-Glahn, Vera and Egozcue, Juan Jos{\'{e}} and Marguerat, Samuel and B{\"{a}}hler, J{\"{u}}rg},
+doi = {10.1371/journal.pcbi.1004075},
+issn = {15537358},
+journal = {{PLoS Computational Biology}},
+number = {3},
+pages = {1--12},
+pmid = {25775355},
+publisher = {{Public Library of Science}},
+title = {{Proportionality: A Valid Alternative to Correlation for Relative Data}},
+volume = {11},
+year = {2015}
+}
+
+
+@article{liu2010stability,
+author = {Liu, Han and Roeder, Kathryn and Wasserman, Larry},
+doi = {10.48550/arxiv.1006.3316},
+journal = {{Advances in Neural Information Processing Systems}},
+title = {{Stability Approach to Regularization Selection (StARS) for High Dimensional Graphical Models}},
+year = {2010}
+}
+
+
+@article{badri2020shrinkage,
+author = {Badri, Michelle and Kurtz, Zachary D. and Bonneau, Richard and M{\"{u}}ller, Christian L.},
+doi = {10.1093/NARGAB/LQAA100},
+issn = {26319268},
+journal = {{NAR Genomics and Bioinformatics}},
+month = {dec},
+number = {4},
+publisher = {{Oxford Academic}},
+title = {{Shrinkage improves estimation of microbial associations under different normalization methods}},
+volume = {2},
+year = {2020}
+}
+
+
+@article{fang2015cclasso,
+author = {Fang, Huaying and Huang, Chengcheng and Zhao, Hongyu and Deng, Minghua},
+doi = {10.1093/bioinformatics/btv349},
+journal = {Bioinformatics},
+number = {19},
+pages = {3172--3180},
+title = {{CCLasso: Correlation inference for compositional data through Lasso}},
+volume = {31},
+year = {2015}
+}
+
+
+@article{faust2012microbial,
+author = {Faust, Karoline and Sathirapongsasuti, J. Fah and Izard, Jacques and Segata, Nicola and Gevers, Dirk and Raes, Jeroen and Huttenhower, Curtis},
+doi = {10.1371/journal.pcbi.1002606},
+journal = {{PLoS Computational Biology}},
+month = {jul},
+number = {7},
+pages = {e1002606},
+publisher = {{Public Library of Science}},
+title = {{Microbial Co-occurrence Relationships in the Human Microbiome}},
+volume = {8},
+year = {2012}
+}
+
+
+@article{fang2017gcoda,
+author = {Fang, H and Huang, C and Zhao, H and Deng, M},
+doi = {10.1089/cmb.2017.0054},
+issn = {10665277},
+journal = {{Journal of Computational Biology}},
+number = {7},
+pages = {699--708},
+title = {{gCoda: Conditional Dependence Network Inference for Compositional Data}},
+volume = {24},
+year = {2017}
+}
+
+@article{lichtblau2017comparative,
+author = {Lichtblau, Yvonne and Zimmermann, Karin and Haldemann, Berit and Lenze, Dido and Hummel, Michael and Leser, Ulf},
+doi = {10.1093/bib/bbw061},
+journal = {{Briefings in Bioinformatics}},
+number = {5},
+pages = {837--850},
+title = {{Comparative assessment of differential network analysis methods}},
+volume = {18},
+year = {2017}
+}
+
+
+@article{jardim2019bionetstat,
+author = {Jardim, Vin{\'{i}}cius Carvalho and {De Siqueira Santos}, Suzana and Fujita, Andre and Buckeridge, Marcos Silveira},
+doi = {10.3389/fgene.2019.00594},
+journal = {{Frontiers in Genetics}},
+number = {JUN},
+pages = {1--13},
+title = {{BioNetStat: A tool for biological networks differential analysis}},
+volume = {10},
+year = {2019}
+}
+
+
+@article{he2019statistical,
+author = {He, Hao and Cao, Shaolong and gang Zhang, Ji and Shen, Hui and Wang, Yu Ping and wen Deng, Hong},
+doi = {10.1038/s41598-019-47362-7},
+journal = {{Scientific Reports}},
+month = {dec},
+number = {1},
+pages = {1--8},
+pmid = {31350445},
+publisher = {{Nature Publishing Group}},
+title = {{A Statistical Test for Differential Network Analysis Based on Inference of Gaussian Graphical Model}},
+volume = {9},
+year = {2019}
+}
+
+
+@article{yu2019new,
+author = {Yu, Danyang and Zhang, Zeyu and Glass, Kimberly and Su, Jessica and DeMeo, Dawn L. and Tantisira, Kelan and Weiss, Scott T. and Qiu, Weiliang},
+doi = {10.1038/s41598-019-40167-8},
+journal = {{Scientific Reports}},
+number = {1},
+pages = {1--12},
+pmid = {30837613},
+title = {{New Statistical Methods for Constructing Robust Differential Correlation Networks to characterize the interactions among microRNAs}},
+volume = {9},
+year = {2019}
+}
+
+
+@article{mckenzie2016dgca,
+author = {McKenzie, Andrew T. and Katsyv, Igor and Song, Won Min and Wang, Minghui and Zhang, Bin},
+doi = {10.1186/s12918-016-0349-1},
+journal = {{BMC Systems Biology}},
+number = {1},
+pages = {1--25},
+publisher = {{BMC Systems Biology}},
+title = {{DGCA: A comprehensive R package for Differential Gene Correlation Analysis}},
+volume = {10},
+year = {2016}
+}
+
+
+@article{siska2017differential,
+author = {Siska, Charlotte and Kechris, Katerina},
+doi = {10.1186/s13104-016-2331-9},
+journal = {{BMC Research Notes}},
+number = {1},
+pages = {1--9},
+pmid = {28103954},
+publisher = {{BioMed Central}},
+title = {{Differential correlation for sequencing data}},
+volume = {10},
+year = {2017}
+}
+
+
+@article{bhuva2019differential,
+author = {Bhuva, Dharmesh D. and Cursons, Joseph and Smyth, Gordon K. and Davis, Melissa J.},
+doi = {10.1186/S13059-019-1851-8},
+journal = {{Genome Biology}},
+month = {nov},
+number = {1},
+pmid = {31727119},
+publisher = {{BMC}},
+title = {{Differential co-expression-based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancer}},
+volume = {20},
+year = {2019}
+}
+
+
+@article{gill2010statistical,
+author = {Gill, Ryan and Datta, Somnath and Datta, Susmita},
+journal = {{BMC Bioinformatics}},
+number = {1},
+pages = {95},
+title = {{A statistical framework for differential network analysis from microarray data}},
+volume = {11},
+year = {2010}
+}
+
+
+@article{shojaie2021differential,
+author = {Shojaie, Ali},
+doi = {10.1002/WICS.1508},
+journal = {{Wiley Interdisciplinary Reviews: Computational Statistics}},
+month = {mar},
+number = {2},
+pages = {e1508},
+publisher = {{John Wiley & Sons, Ltd}},
+title = {{Differential network analysis: A statistical perspective}},
+volume = {13},
+year = {2021}
+}
+
+
+@incollection{fisher1970statistical,
+  title={Statistical methods for research workers},
+  author={Fisher, Ronald Aylmer},
+  booktitle={{Breakthroughs in statistics: Methodology and distribution}},
+  pages={66--70},
+  year={1970},
+  publisher={Springer}
+}
+
+
+@article{siska2016discordant,
+author = {Siska, Charlotte and Bowler, Russell and Kechris, Katerina},
+doi = {10.1093/bioinformatics/btv633},
+journal = {Bioinformatics},
+number = {5},
+pages = {690--696},
+title = {{The discordant method: A novel approach for differential correlation}},
+volume = {32},
+year = {2016},
+publisher={{Oxford University Press}}
+}
+
+
+@article{yaverouglu2014revealing,
+author = {Yavero{\u{g}}lu, {\"O}mer Nebil and Malod-Dognin, No{\"e}l and Davis, Darren and Levnajic, Zoran and Janjic, Vuk and Karapandza, Rasa and Stojmirovic, Aleksandar and Pr{\v{z}}ulj, Nata{\v{s}}a},
+doi = {10.1038/srep04547},
+journal = {{Scientific Reports}},
+month = {apr},
+number = {1},
+pages = {1--9},
+publisher = {{Nature Publishing Group}},
+title = {{Revealing the Hidden Language of Complex Networks}},
+volume = {4},
+year = {2014}
+}