diff --git a/_site.yml b/_site.yml index 89700221..d67ba77f 100644 --- a/_site.yml +++ b/_site.yml @@ -24,24 +24,7 @@ navbar: href: home_content.html - text: Precourse href: home_precourse.html -output: - bookdown::html_document2: - highlight: textmate - toc: true - toc_float: - collapsed: true - smooth_scroll: true - print: false - toc_depth: 4 - number_sections: true - df_print: default - code_folding: none - self_contained: false - keep_md: false - encoding: 'UTF-8' - css: "assets/lab.css" - include: - after_body: assets/footer-lab.html + # r packages needed for the workshop # used in home_precourse.Rmd # split into cran and bioc packages diff --git a/home_content.Rmd b/home_content.Rmd index a29ca306..a9fc5086 100644 --- a/home_content.Rmd +++ b/home_content.Rmd @@ -2,8 +2,22 @@ title: "Content" output: bookdown::html_document2: + highlight: textmate toc: false + toc_float: + collapsed: true + smooth_scroll: true + print: false + toc_depth: 4 number_sections: false + df_print: default + code_folding: none + self_contained: false + keep_md: false + encoding: 'UTF-8' + css: "assets/lab.css" + include: + after_body: assets/footer-lab.html --- ```{r,child="assets/header-lab.Rmd"} diff --git a/home_info.Rmd b/home_info.Rmd index b683cc89..82d3b574 100644 --- a/home_info.Rmd +++ b/home_info.Rmd @@ -2,8 +2,22 @@ title: "Info" output: bookdown::html_document2: + highlight: textmate toc: false + toc_float: + collapsed: true + smooth_scroll: true + print: false + toc_depth: 4 number_sections: false + df_print: default + code_folding: none + self_contained: false + keep_md: false + encoding: 'UTF-8' + css: "assets/lab.css" + include: + after_body: assets/footer-lab.html --- ```{r,child="assets/header-lab.Rmd"} diff --git a/home_precourse.Rmd b/home_precourse.Rmd index fcf26191..c20b9bf0 100644 --- a/home_precourse.Rmd +++ b/home_precourse.Rmd @@ -2,8 +2,22 @@ title: "Precourse" output: bookdown::html_document2: + highlight: textmate toc: false + toc_float: + collapsed: true + smooth_scroll: true + print: false + toc_depth: 4 number_sections: false + df_print: default + code_folding: none + self_contained: false + keep_md: false + encoding: 'UTF-8' + css: "assets/lab.css" + include: + after_body: assets/footer-lab.html --- ```{r,child="assets/header-lab.Rmd"} diff --git a/home_schedule.Rmd b/home_schedule.Rmd index c5f0e6f6..73da6727 100644 --- a/home_schedule.Rmd +++ b/home_schedule.Rmd @@ -2,8 +2,22 @@ title: "Schedule" output: bookdown::html_document2: + highlight: textmate toc: false + toc_float: + collapsed: true + smooth_scroll: true + print: false + toc_depth: 4 number_sections: false + df_print: default + code_folding: none + self_contained: false + keep_md: false + encoding: 'UTF-8' + css: "assets/lab.css" + include: + after_body: assets/footer-lab.html --- ```{r,child="assets/header-lab.Rmd"} diff --git a/index.Rmd b/index.Rmd index b4f54833..559017ec 100644 --- a/index.Rmd +++ b/index.Rmd @@ -2,8 +2,22 @@ title: " " output: bookdown::html_document2: + highlight: textmate toc: false + toc_float: + collapsed: true + smooth_scroll: true + print: false + toc_depth: 4 number_sections: false + df_print: default + code_folding: none + self_contained: false + keep_md: false + encoding: 'UTF-8' + css: "assets/lab.css" + include: + after_body: assets/footer-lab.html --- ```{r,child="assets/header-lab.Rmd"} diff --git a/lab_annotation.Rmd b/lab_annotation.Rmd index e219cc6a..814dd89b 100644 --- a/lab_annotation.Rmd +++ b/lab_annotation.Rmd @@ -1,6 +1,24 @@ --- title: "Transcriptome annotation" subtitle: "Workshop on RNA-Seq" +output: + bookdown::html_document2: + highlight: textmate + toc: true + toc_float: + collapsed: true + smooth_scroll: true + print: false + toc_depth: 4 + number_sections: true + df_print: default + code_folding: none + self_contained: false + keep_md: false + encoding: 'UTF-8' + css: "assets/lab.css" + include: + after_body: assets/footer-lab.html --- ```{r,child="assets/header-lab.Rmd"} diff --git a/lab_assembly.Rmd b/lab_assembly.Rmd index 4615cd92..53b0b15b 100644 --- a/lab_assembly.Rmd +++ b/lab_assembly.Rmd @@ -1,6 +1,24 @@ --- title: "Transcriptome assembly" subtitle: "Workshop on RNA-Seq" +output: + bookdown::html_document2: + highlight: textmate + toc: true + toc_float: + collapsed: true + smooth_scroll: true + print: false + toc_depth: 4 + number_sections: true + df_print: default + code_folding: none + self_contained: false + keep_md: false + encoding: 'UTF-8' + css: "assets/lab.css" + include: + after_body: assets/footer-lab.html --- ```{r,child="assets/header-lab.Rmd"} diff --git a/lab_dge.Rmd b/lab_dge.Rmd index 13e91836..7b68baca 100644 --- a/lab_dge.Rmd +++ b/lab_dge.Rmd @@ -3,6 +3,24 @@ title: "Differential Gene Expression" subtitle: "Workshop on RNA-Seq" editor_options: chunk_output_type: console +output: + bookdown::html_document2: + highlight: textmate + toc: true + toc_float: + collapsed: true + smooth_scroll: true + print: false + toc_depth: 4 + number_sections: true + df_print: default + code_folding: none + self_contained: false + keep_md: false + encoding: 'UTF-8' + css: "assets/lab.css" + include: + after_body: assets/footer-lab.html --- ```{r,child="assets/header-lab.Rmd"} diff --git a/lab_download.Rmd b/lab_download.Rmd index 639b390a..100b8a86 100644 --- a/lab_download.Rmd +++ b/lab_download.Rmd @@ -1,6 +1,24 @@ --- title: "Annotation data" subtitle: Workshop on RNA-Seq +output: + bookdown::html_document2: + highlight: textmate + toc: true + toc_float: + collapsed: true + smooth_scroll: true + print: false + toc_depth: 4 + number_sections: true + df_print: default + code_folding: none + self_contained: false + keep_md: false + encoding: 'UTF-8' + css: "assets/lab.css" + include: + after_body: assets/footer-lab.html --- ```{r,child="assets/header-lab.Rmd"} diff --git a/lab_eda.Rmd b/lab_eda.Rmd index 826c048c..803073a2 100644 --- a/lab_eda.Rmd +++ b/lab_eda.Rmd @@ -3,6 +3,24 @@ title: "PCA and Clustering" subtitle: "Workshop on RNA-Seq" editor_options: chunk_output_type: console +output: + bookdown::html_document2: + highlight: textmate + toc: true + toc_float: + collapsed: true + smooth_scroll: true + print: false + toc_depth: 4 + number_sections: true + df_print: default + code_folding: none + self_contained: false + keep_md: false + encoding: 'UTF-8' + css: "assets/lab.css" + include: + after_body: assets/footer-lab.html --- ```{r,child="assets/header-lab.Rmd"} diff --git a/lab_functional.Rmd b/lab_functional.Rmd index 5ff10802..581bbe43 100644 --- a/lab_functional.Rmd +++ b/lab_functional.Rmd @@ -3,6 +3,24 @@ title: "Gene Function Annotation" subtitle: Workshop on RNA-Seq editor_options: chunk_output_type: console +output: + bookdown::html_document2: + highlight: textmate + toc: true + toc_float: + collapsed: true + smooth_scroll: true + print: false + toc_depth: 4 + number_sections: true + df_print: default + code_folding: none + self_contained: false + keep_md: false + encoding: 'UTF-8' + css: "assets/lab.css" + include: + after_body: assets/footer-lab.html --- ```{r,child="assets/header-lab.Rmd"} diff --git a/lab_geoquery.Rmd b/lab_geoquery.Rmd index 3e925cb8..e0fd699c 100644 --- a/lab_geoquery.Rmd +++ b/lab_geoquery.Rmd @@ -3,6 +3,24 @@ title: "Online Repositories" subtitle: "Workshop on RNA-Seq" editor_options: chunk_output_type: console +output: + bookdown::html_document2: + highlight: textmate + toc: true + toc_float: + collapsed: true + smooth_scroll: true + print: false + toc_depth: 4 + number_sections: true + df_print: default + code_folding: none + self_contained: false + keep_md: false + encoding: 'UTF-8' + css: "assets/lab.css" + include: + after_body: assets/footer-lab.html --- ```{r,child="assets/header-lab.Rmd"} diff --git a/lab_igv.Rmd b/lab_igv.Rmd index 0bad7116..995de86a 100644 --- a/lab_igv.Rmd +++ b/lab_igv.Rmd @@ -1,6 +1,24 @@ --- title: "Using IGV" subtitle: "Workshop on RNA-Seq" +output: + bookdown::html_document2: + highlight: textmate + toc: true + toc_float: + collapsed: true + smooth_scroll: true + print: false + toc_depth: 4 + number_sections: true + df_print: default + code_folding: none + self_contained: false + keep_md: false + encoding: 'UTF-8' + css: "assets/lab.css" + include: + after_body: assets/footer-lab.html --- ```{r,child="assets/header-lab.Rmd"} diff --git a/lab_kallisto.Rmd b/lab_kallisto.Rmd index c14ff08f..2135159e 100644 --- a/lab_kallisto.Rmd +++ b/lab_kallisto.Rmd @@ -1,6 +1,24 @@ --- title: 'Kallisto ' subtitle: Workshop on RNA-Seq +output: + bookdown::html_document2: + highlight: textmate + toc: true + toc_float: + collapsed: true + smooth_scroll: true + print: false + toc_depth: 4 + number_sections: true + df_print: default + code_folding: none + self_contained: false + keep_md: false + encoding: 'UTF-8' + css: "assets/lab.css" + include: + after_body: assets/footer-lab.html --- ```{r,child="assets/header-lab.Rmd"} diff --git a/lab_mapping.Rmd b/lab_mapping.Rmd index af2a2166..42ae94e4 100644 --- a/lab_mapping.Rmd +++ b/lab_mapping.Rmd @@ -1,6 +1,24 @@ --- title: "Mapping" subtitle: "Workshop on RNA-Seq" +output: + bookdown::html_document2: + highlight: textmate + toc: true + toc_float: + collapsed: true + smooth_scroll: true + print: false + toc_depth: 4 + number_sections: true + df_print: default + code_folding: none + self_contained: false + keep_md: false + encoding: 'UTF-8' + css: "assets/lab.css" + include: + after_body: assets/footer-lab.html --- ```{r,child="assets/header-lab.Rmd"} diff --git a/lab_preprocessing.Rmd b/lab_preprocessing.Rmd index abf18fba..81fcbe2c 100644 --- a/lab_preprocessing.Rmd +++ b/lab_preprocessing.Rmd @@ -3,6 +3,24 @@ title: "Data preprocessing" subtitle: Workshop on RNA-Seq editor_options: chunk_output_type: console +output: + bookdown::html_document2: + highlight: textmate + toc: true + toc_float: + collapsed: true + smooth_scroll: true + print: false + toc_depth: 4 + number_sections: true + df_print: default + code_folding: none + self_contained: false + keep_md: false + encoding: 'UTF-8' + css: "assets/lab.css" + include: + after_body: assets/footer-lab.html --- ```{r,child="assets/header-lab.Rmd"} diff --git a/lab_qc_aftermapping.Rmd b/lab_qc_aftermapping.Rmd index d732f35e..2613ebd0 100644 --- a/lab_qc_aftermapping.Rmd +++ b/lab_qc_aftermapping.Rmd @@ -1,6 +1,24 @@ --- title: "Quality control" subtitle: "Workshop on RNA-Seq" +output: + bookdown::html_document2: + highlight: textmate + toc: true + toc_float: + collapsed: true + smooth_scroll: true + print: false + toc_depth: 4 + number_sections: true + df_print: default + code_folding: none + self_contained: false + keep_md: false + encoding: 'UTF-8' + css: "assets/lab.css" + include: + after_body: assets/footer-lab.html --- ```{r,child="assets/header-lab.Rmd"} diff --git a/lab_qc_beforemapping.Rmd b/lab_qc_beforemapping.Rmd index dd4e46a7..ab32c5f8 100644 --- a/lab_qc_beforemapping.Rmd +++ b/lab_qc_beforemapping.Rmd @@ -1,6 +1,24 @@ --- title: "Quality control before mapping" subtitle: Workshop on RNA-Seq +output: + bookdown::html_document2: + highlight: textmate + toc: true + toc_float: + collapsed: true + smooth_scroll: true + print: false + toc_depth: 4 + number_sections: true + df_print: default + code_folding: none + self_contained: false + keep_md: false + encoding: 'UTF-8' + css: "assets/lab.css" + include: + after_body: assets/footer-lab.html --- ```{r,child="assets/header-lab.Rmd"} diff --git a/lab_quantification.Rmd b/lab_quantification.Rmd index 11101f02..65879d99 100644 --- a/lab_quantification.Rmd +++ b/lab_quantification.Rmd @@ -3,8 +3,22 @@ title: "Quantification" subtitle: "Workshop on RNA-Seq" output: bookdown::html_document2: + highlight: textmate toc: false + toc_float: + collapsed: true + smooth_scroll: true + print: false + toc_depth: 4 number_sections: false + df_print: default + code_folding: none + self_contained: false + keep_md: false + encoding: 'UTF-8' + css: "assets/lab.css" + include: + after_body: assets/footer-lab.html --- ```{r,child="assets/header-lab.Rmd"} diff --git a/lab_r.Rmd b/lab_r.Rmd index c21a7c75..c9199f19 100644 --- a/lab_r.Rmd +++ b/lab_r.Rmd @@ -1,6 +1,24 @@ --- title: "Intro to R" subtitle: "Workshop on RNA-Seq" +output: + bookdown::html_document2: + highlight: textmate + toc: true + toc_float: + collapsed: true + smooth_scroll: true + print: false + toc_depth: 4 + number_sections: true + df_print: default + code_folding: none + self_contained: false + keep_md: false + encoding: 'UTF-8' + css: "assets/lab.css" + include: + after_body: assets/footer-lab.html --- ```{r,child="assets/header-lab.Rmd"} diff --git a/lab_smallrna.Rmd b/lab_smallrna.Rmd index b1f61ec5..46b3110f 100644 --- a/lab_smallrna.Rmd +++ b/lab_smallrna.Rmd @@ -1,6 +1,24 @@ --- title: "Small RNA-Seq Analysis" subtitle: "Workshop on RNA-Seq" +output: + bookdown::html_document2: + highlight: textmate + toc: true + toc_float: + collapsed: true + smooth_scroll: true + print: false + toc_depth: 4 + number_sections: true + df_print: default + code_folding: none + self_contained: false + keep_md: false + encoding: 'UTF-8' + css: "assets/lab.css" + include: + after_body: assets/footer-lab.html --- ```{r,child="assets/header-lab.Rmd"} diff --git a/lab_uppmax_intro.Rmd b/lab_uppmax_intro.Rmd index f4a0d112..f7952ad5 100644 --- a/lab_uppmax_intro.Rmd +++ b/lab_uppmax_intro.Rmd @@ -1,5 +1,23 @@ --- title: 'Working on UPPMAX' +output: + bookdown::html_document2: + highlight: textmate + toc: true + toc_float: + collapsed: true + smooth_scroll: true + print: false + toc_depth: 4 + number_sections: true + df_print: default + code_folding: none + self_contained: false + keep_md: false + encoding: 'UTF-8' + css: "assets/lab.css" + include: + after_body: assets/footer-lab.html --- ```{r,child="assets/header-lab.Rmd"}