diff fastqc_report.Rmd @ 0:b7c115edd970 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastqc_report.Rmd	Tue Feb 27 10:37:12 2018 -0500
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+---
+title: 'Short reads evaluation with [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)'
+output:
+    html_document:
+      number_sections: true
+      toc: true
+      theme: cosmo
+      highlight: tango
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(
+  echo = as.logical(opt$X_e),
+  error = TRUE,
+  eval = TRUE
+)
+```
+
+
+
+
+
+##
+
+##
+
+
+##
+
+
+##
+
+##
+
+##
+
+### Kmer Content {.tabset}
+
+#### Before
+
+```{r 'Kmer Content (before)', fig.width=10}
+kc_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Kmer Content')
+knitr::kable(kc_1)
+```
+
+#### After
+```{r 'Kmer Content (after)', fig.width=10}
+kc_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Kmer Content')
+knitr::kable(kc_2)
+```
+
+
+# Session Info
+
+```{r 'session info'}
+sessionInfo()
+```
+
+# References
+
+* 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