| Previous changeset 14:a6bf4dfca096 (2017-11-09) |
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Commit message:
remove unnecessary dependencies |
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modified:
fastqc_site.xml fastqc_site_render.R index.Rmd |
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| diff -r a6bf4dfca096 -r a6f8382f852c fastqc_site.xml --- a/fastqc_site.xml Thu Nov 09 09:32:42 2017 -0500 +++ b/fastqc_site.xml Thu Nov 09 09:49:39 2017 -0500 |
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| @@ -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> |
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| diff -r a6bf4dfca096 -r a6f8382f852c fastqc_site_render.R --- 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 |
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| @@ -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 ============== |
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| diff -r a6bf4dfca096 -r a6f8382f852c index.Rmd --- a/index.Rmd Thu Nov 09 09:32:42 2017 -0500 +++ b/index.Rmd Thu Nov 09 09:49:39 2017 -0500 |
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| @@ -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 + |