Mercurial > repos > mingchen0919 > aurora_fastqc_site
changeset 1:92e3de11b9f8 draft
remove fastqc_report.Rmd
author | mingchen0919 |
---|---|
date | Tue, 27 Feb 2018 10:40:20 -0500 |
parents | b7c115edd970 |
children | c64267b9f754 |
files | fastqc_report.Rmd |
diffstat | 1 files changed, 0 insertions(+), 69 deletions(-) [+] |
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--- a/fastqc_report.Rmd Tue Feb 27 10:37:12 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,69 +0,0 @@ ---- -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