Publish WGCNA example!

Snakefile

@@ -17,7 +17,9 @@ rule target:
         "03-rnaseq/dimension-reduction_rnaseq_02_umap.html",
         "03-rnaseq/gene-id-annotation_rnaseq_01_ensembl.html",
         "03-rnaseq/ortholog-mapping_rnaseq_01_ensembl.html",
-        "04-advanced-topics/00-intro-to-advanced-topics.html"
+        "04-advanced-topics/00-intro-to-advanced-topics.html",
+        "04-advanced-topics/network-analysis_rnaseq_01_wgcna.html"
+
 
 rule render_citations:
     input:

components/_navbar.html

@@ -61,7 +61,7 @@
             <ul class="dropdown-menu">
               <!-- Individual Advanced topics pages go in this list -->
               <li><a href="../04-advanced-topics/00-intro-to-advanced-topics.html">Introduction</a></li>
-
+              <li><a href="../04-advanced-topics/network-analysis_rnaseq_01_wgcna.html">Network Analysis - WGCNA</a></li>
             </ul>
 
         </li><!--/advanced dropdown-->

components/dictionary.txt

@@ -16,6 +16,7 @@ Brainarray’s
 Brems
 CCDL
 CCDL's
+cDNA
 cheatsheet
 cheatsheets
 ChIP
@@ -24,6 +25,7 @@ Cmd
 ColorBrewer
 Compara
 ComplexHeatmap
+ComplexHeatmap's
 CREB
 Crouser
 cytosolic
@@ -44,6 +46,7 @@ duplications
 ECM
 edgeR
 edgeR's
+eigengene
 e.g.
 ENSDARG
 Ensembl
@@ -79,14 +82,16 @@ JPEG
 KEGG
 limma
 logFC
+maxBlockSize
 medulloblastoma
 microarray’s
 molecularly
 musculus
 MSigDB
 myeloid
-Northcott
 nb
+NES
+Northcott
 ortholog
 orthologs
 orthology
@@ -132,6 +137,8 @@ unmapped
 upregulated
 UpSet
 vivo
+WGCNA
+WGCNA's
 WNT
 Yaari
 zebrafish

components/references.bib

@@ -6,7 +6,21 @@ @manual{Ahlmann-Eltze2020
   note   = {R package version 0.3.0},
   url    = {https://github.com/const-ae/ggupset}
 }
-
+
+@article{Alter2000,
+  doi = {10.1073/pnas.97.18.10101},
+  url = {https://doi.org/10.1073/pnas.97.18.10101},
+  year = {2000},
+  month = aug,
+  publisher = {Proceedings of the National Academy of Sciences},
+  volume = {97},
+  number = {18},
+  pages = {10101--10106},
+  author = {O. Alter and P. O. Brown and D. Botstein},
+  title = {Singular value decomposition for genome-wide expression data processing and modeling},
+  journal = {Proceedings of the National Academy of Sciences}
+}
+
 @website{annotation-packages,
   title  = {Packages found under {AnnotationData}},
   author = {{R Bioconductor Team}},
@@ -232,6 +246,14 @@ @article{Hansen2010
   url     = {https://pubmed.ncbi.nlm.nih.gov/20395217/}
 }
 
+@manual{Hastie2020,
+    title = {impute: Imputation for microarray data},
+    author = {Trevor Hastie and Robert Tibshirani and Balasubramanian Narasimhan and Gilbert Chu},
+    year = {2020},
+    note = {R package version 1.64.0},
+    url = {https://www.bioconductor.org/packages/devel/bioc/manuals/impute/man/impute.pdf},
+  }
+
 @website{hcop-help,
   title  = {HCOP help},
   author = {{HGNC Team}},
@@ -280,6 +302,12 @@ @article{Kanehisa2000
   url     = {https://www.genome.jp/kegg/}
 }
 
+@website{KhanAcademy,
+  author  = {Khan Academy},
+  title   = {Introduction to eigenvalues and eigenvectors},
+  url     = {https://www.khanacademy.org/math/linear-algebra/alternate-bases/eigen-everything/v/linear-algebra-introduction-to-eigenvalues-and-eigenvectors}
+}
+
 @article{Khatri2012,
   author  = {Khatri, P.  and Sirota, M.  and Butte, A. J. },
   title   = {Ten years of pathway analysis: current approaches and outstanding challenges},
@@ -315,6 +343,58 @@ @manual{Konopka2020
   url    = {https://cran.r-project.org/web/packages/umap/umap.pdf}
 }
 
+@article{Korotkevich2019,
+  author  = {Gennady Korotkevich and Vladimir Sukhov and Alexey Sergushichev},
+  title   = {Fast gene set enrichment analysis},
+  journal = {bioRxiv},
+  year    = {2019},
+  number  = {060012},
+  doi     = {10.1101/060012},
+  url     = {https://doi.org/10.1101/060012}
+}
+
+@article{Langfelder2007,
+  doi = {10.1186/1752-0509-1-54},
+  url = {https://doi.org/10.1186/1752-0509-1-54},
+  year = {2007},
+  month = nov,
+  publisher = {Springer Science and Business Media {LLC}},
+  volume = {1},
+  number = {1},
+  author = {Peter Langfelder and Steve Horvath},
+  title = {Eigengene networks for studying the relationships between co-expression modules},
+  journal = {{BMC} Systems Biology}
+}
+
+@article{Langfelder2008,
+  doi = {10.1186/1471-2105-9-559},
+  url = {https://doi.org/10.1186/1471-2105-9-559},
+  year = {2008},
+  month = dec,
+  publisher = {Springer Science and Business Media {LLC}},
+  volume = {9},
+  number = {1},
+  author = {Peter Langfelder and Steve Horvath},
+  title = {{WGCNA}: an R package for weighted correlation network analysis},
+  journal = {{BMC} Bioinformatics}
+}
+
+@article{Langfelder2016,
+  url = {https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/},
+  year = {2016},
+  month = Feb,
+  author = {Peter Langfelder and Steve Horvath},
+  title = {Tutorials for the {WGCNA} package},
+}
+
+@website{Langfelder2018,
+  url = {https://peterlangfelder.com/2018/11/25/signed-or-unsigned-which-network-type-is-preferable/},
+  year = {2018},
+  month = Nov,
+  author = {Peter Langfelder},
+  title = {Signed or unsigned: which network type is preferable?},
+}
+
 @website{LCSciences2014,
   title  = {Microarray or {RNA} Sequencing?},
   author = {LCSciences},
@@ -455,6 +535,14 @@ @website{pca-visually-explained
   url    = {https://setosa.io/ev/principal-component-analysis/}
 }
 
+@manual{Pedersen2020,
+    title = {ggforce: Accelerating 'ggplot2'},
+    author = {Thomas Lin Pedersen},
+    year = {2020},
+    url = {https://ggforce.data-imaginist.com},
+    github = {https://github.com/thomasp85/ggforce},
+  }
+
 @article{Pepke2009,
   author  = {Pepke, S.  and Wold, B.  and Mortazavi, A. },
   title   = {Computation for {ChIP-seq} and {RNA-seq} studies},
@@ -760,6 +848,19 @@ @article{Yu2012
   url     = {https://doi.org/10.1089/omi.2011.0118}
 }
 
+@article{Zhang2005,
+  doi = {10.2202/1544-6115.1128},
+  url = {https://doi.org/10.2202/1544-6115.1128},
+  year = {2005},
+  month = jan,
+  publisher = {Walter de Gruyter {GmbH}},
+  volume = {4},
+  number = {1},
+  author = {Bin Zhang and Steve Horvath},
+  title = {A General Framework for Weighted Gene Co-Expression Network Analysis},
+  journal = {Statistical Applications in Genetics and Molecular Biology}
+}
+
 @article{Zhang2017,
   author  = {Zhang, C.  and Zhang, B.  and Lin, L. L.  and Zhao, S. },
   title   = {Evaluation and comparison of computational tools for {RNA-seq} isoform quantification},

docker/Dockerfile

@@ -49,7 +49,7 @@ RUN Rscript -e  "install.packages( \
 
 # Install bioconductor packages
 # org.Mm.eg.db and org.Dr.eg.db are required for gene mapping
-RUN R -e "options(warn = 2); BiocManager::install( \
+RUN Rscript -e "options(warn = 2); BiocManager::install( \
     c('affy', \
       'apeglm', \
       'Biobase', \
@@ -58,6 +58,7 @@ RUN R -e "options(warn = 2); BiocManager::install( \
       'DESeq2', \
       'EnhancedVolcano', \
       'ggupset', \
+      'impute', \
       'limma', \
       'marray', \
       'msigdbr', \
@@ -81,6 +82,9 @@ RUN Rscript -e  "install.packages( \
 # Need this package to make plots colorblind friendly
 RUN Rscript -e "remotes::install_github('clauswilke/colorblindr', ref = '1ac3d4d62dad047b68bb66c06cee927a4517d678', dependencies = TRUE)"
 
+# Install WGCNA
+RUN Rscript -e  "options(warn = 2); install.packages('WGCNA')"
+
 # Install python libraries
 ##########################