WGCNA Part 1: Set up (#358)

* Put in basic changes: navbar, dict, snakefile, Rmd

* More polishing and info and refs

* Update file paths

* Bring back docker changes

* Add to dictionary

* Add a couple refs

* Add ref and other little things

* Revert "Add ref and other little things"

This reverts commit 7560c2a.

* Address straightforward comments from cbethell

* Add ref

* Add more refs and re-render

* Remove that extra part that should only be in part2 not here

* Incorporate jashapiro review

* Shorten up some more comments

* rowSums!!

* Get rid of tibble step and change wording

Snakefile

@@ -18,7 +18,9 @@ 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

@@ -62,7 +62,7 @@
             <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

@@ -45,6 +45,7 @@ duplications
 ECM
 edgeR
 edgeR's
+eigengene
 e.g.
 ENSDARG
 Ensembl
@@ -80,15 +81,16 @@ JPEG
 KEGG
 limma
 logFC
+maxBlockSize
 medulloblastoma
 microarray’s
 molecularly
 musculus
 MSigDB
 myeloid
+nb
 NES
 Northcott
-nb
 ortholog
 orthologs
 orthology
@@ -137,6 +139,8 @@ 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}},
@@ -238,6 +252,14 @@ @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}},
@@ -286,6 +308,12 @@ @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},
@@ -331,6 +359,48 @@ @article{Korotkevich2019
   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},
@@ -787,6 +857,19 @@ @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

@@ -35,6 +35,9 @@ RUN pip3 install \
 #### R packages
 ###############
 
+# We need to install impute so WGCNA will install in the next step
+RUN R -e "options(warn = 2); BiocManager::install('impute', update = FALSE)"
+
 # Commonly used R packages
 RUN Rscript -e  "install.packages( \
     c('cluster', \
@@ -45,7 +48,8 @@ RUN Rscript -e  "install.packages( \
       'rprojroot', \
       'viridis', \
       'spelling', \
-      'styler'))"
+      'styler', \
+      'WGCNA'))"
 
 # Install bioconductor packages
 # org.Mm.eg.db and org.Dr.eg.db are required for gene mapping