changeset 15:a6f8382f852c draft default tip

remove unnecessary dependencies

--- a/fastqc_site.xml	Thu Nov 09 09:32:42 2017 -0500
+++ b/fastqc_site.xml	Thu Nov 09 09:49:39 2017 -0500
@@ -122,15 +122,13 @@
             }
         </citation>
         <citation type="bibtex">
-            @article{ewels2016multiqc,
-            title={MultiQC: summarize analysis results for multiple tools and samples in a single report},
-            author={Ewels, Philip and Magnusson, M{\aa}ns and Lundin, Sverker and K{\"a}ller, Max},
-            journal={Bioinformatics},
-            volume={32},
-            number={19},
-            pages={3047--3048},
-            year={2016},
-            publisher={Oxford University Press}
+            @Book{ggplot22016,
+            author = {Hadley Wickham},
+            title = {ggplot2: Elegant Graphics for Data Analysis},
+            publisher = {Springer-Verlag New York},
+            year = {2009},
+            isbn = {978-0-387-98140-6},
+            url = {http://ggplot2.org},
             }
         </citation>
     </citations>

--- a/fastqc_site_render.R	Thu Nov 09 09:32:42 2017 -0500
+++ b/fastqc_site_render.R	Thu Nov 09 09:49:39 2017 -0500
@@ -4,11 +4,9 @@
 library(plyr)
 library(dplyr)
 library(stringr)
-library(highcharter)
 library(DT)
 library(reshape2)
 library(plotly)
-library(formattable)
 options(stringsAsFactors=FALSE, useFancyQuotes=FALSE)
 
 ##============ Sink warnings and errors to a file ==============

--- a/index.Rmd	Thu Nov 09 09:32:42 2017 -0500
+++ b/index.Rmd	Thu Nov 09 09:49:39 2017 -0500
@@ -11,10 +11,13 @@
 
 ## References
 
-* Andrews, Simon. "FastQC: a quality control tool for high throughput sequence data." (2010): 175-176.
-* Goecks, Jeremy, Anton Nekrutenko, and James Taylor. "Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences." Genome biology 11.8 (2010): R86.
-* Afgan, Enis, et al. "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update." Nucleic acids research (2016): gkw343.
-* Highcharts. https://www.highcharts.com/. (access by May 26, 2017).
-* R Core Team (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
-* Joshua Kunst (2017). highcharter: A Wrapper for the 'Highcharts' Library. R package version 0.5.0. https://CRAN.R-project.org/package=highcharter
-* Carson Sievert, Chris Parmer, Toby Hocking, Scott Chamberlain, Karthik Ram, Marianne Corvellec and Pedro Despouy (2017). plotly: Create Interactive Web Graphics via 'plotly.js'. R package version 4.6.0. https://CRAN.R-project.org/package=plotly
+* Bioinformatics, Babraham (2014). FastQC.
+
+* Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins, Aron and Hyndman, Rob (2016). rmarkdown: Dynamic Documents for R, 2016. In R package version 0.9, 6.
+
+* Xie, Yihui (2015). Dynamic Documents with R and knitr, CRC Press, Vol.29.
+
+* Carson Sievert and Chris Parmer and Toby Hocking and Scott Chamberlain and Karthik Ram and Marianne Corvellec and Pedro Despouy (2017). plotly: Create Interactive Web Graphics via 'plotly.js'. R package version 4.6.0. [Link]
+
+* Wickham, H. (2016). ggplot2: elegant graphics for data analysis. Springer. Chicago
+