From f412282758f216a6285119975fa4a345ac79ebf9 Mon Sep 17 00:00:00 2001 From: Jian Sheng Boey <95262076+JSBoey@users.noreply.github.com> Date: Wed, 23 Aug 2023 11:42:00 +1200 Subject: [PATCH] Remove grid tables --- docs/index.md | 11 ++++++++++- mkdocs.yml | 1 - 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/docs/index.md b/docs/index.md index 19808555..5831acfb 100644 --- a/docs/index.md +++ b/docs/index.md @@ -13,7 +13,7 @@ | [Day 2](#){ .md-button .md-button--primary } | [1. Introduction to binning](./day2/ex6_initial_binning.md)
[2. Binning with multiple tools](./day2/ex7_initial_binning.md)
[3. Bin dereplication](./day2/ex8_bin_dereplication.md)
[4. Manual bin refinement](./day2/ex9_refining_bins.md) | | [Day 3](#){ .md-button .md-button--primary } | [1. Assigning taxonomy to refined prokaryotic bins](./day3/ex11_coverage_and_taxonomy.md)
[2. Identifying viral contigs in metagenomic data](./day3/ex10_viruses.md)
[3. Gene prediction](./day3/ex12_gene_prediction.md)
[4. Gene annotation I: BLAST-like and HMM](./day3/ex13_gene_annotation_part1.md)
[5. Gene annotation II: DRAM and coverage calculation](./day3/ex14_gene_annotation_part2.md) | | [Day 4](#){ .md-button .md-button--primary } | [1. Gene annotation III](./day4/ex15_gene_annotation_part3.md)
[2. Introduction to data presentation](./day4/ex16a_data_presentation_Intro.md)
[3. Coverage heatmaps](./day4/ex16b_data_presentation_Coverage.md)
[4. Ordinations](./day4/ex16c_OPTIONAL_data_presentation_Ordination.md)
[5. KEGG pathway maps](./day4/ex16d_data_presentation_KEGG_pathways.md)
[6. Gene synteny](./day4/ex16e_data_presentation_Gene_synteny.md)
[7. CAZy heatmaps (optional)](./day4/ex16f_OPTIONAL_data_presentation_CAZy_annotations.md) | ---> + +-------------------------------------------------------------+-----------------------------------------------------------------------------------------------+ |
**Day**
|
**Lesson topic**
| @@ -45,6 +45,15 @@ | | [7. CAZy heatmaps](./day4/ex16f_OPTIONAL_data_presentation_CAZy_annotations.md) | +-------------------------------------------------------------+-----------------------------------------------------------------------------------------------+ +--> + +|
Day
|
Lesson topic
| +| --- | --- | +| [Day 1: Assembly](#){ .md-button .md-button--primary } | [1. (Pre-Summer School) Introduction I: Shell](./day1/ex1_bash_and_scheduler.md)
[2. Introduction II: HPC and job scheduler](./day1/ex2_1_intro_to_scheduler.md)
[3. Filter raw reads by quality](./day1/ex2_quality_filtering.md)
[4. Assembly I: Assembling contigs](./day1/ex3_assembly.md)
[5. Assembly II: Variable parameters](./day1/ex4_assembly.md)
[6. Assembly evaluation](./day1/ex5_evaluating_assemblies.md) | +| [Day 2: Binning](#){ .md-button .md-button--primary } | [1. Introduction to binning](./day2/ex6_initial_binning.md)
[2. Binning with multiple tools](./day2/ex7_initial_binning.md)
[3. Bin dereplication](./day2/ex8_bin_dereplication.md)
[4. Manual bin refinement](./day2/ex9_refining_bins.md) | +| [Day 3: Annotation](#){ .md-button .md-button--primary } | [1. Assigning taxonomy to refined prokaryotic bins](./day3/ex11_coverage_and_taxonomy.md)
[2. Identifying viral contigs in metagenomic data](./day3/ex10_viruses.md)
[3. Gene prediction](./day3/ex12_gene_prediction.md)
[4. Gene annotation I: BLAST-like and HMM](./day3/ex13_gene_annotation_part1.md)
[5. Gene annotation II: DRAM and coverage calculation](./day3/ex14_gene_annotation_part2.md) | +| [Day 4: Visualisation](#){ .md-button .md-button--primary } | [1. Gene annotation III: DRAM distillation](./day4/ex15_gene_annotation_part3.md)
[2. Introduction to data presentation](./day4/ex16a_data_presentation_Intro.md)
[3. Coverage heatmaps](./day4/ex16b_data_presentation_Coverage.md)
[4. Ordinations](./day4/ex16c_OPTIONAL_data_presentation_Ordination.md)
[5. KEGG pathway maps](./day4/ex16d_data_presentation_KEGG_pathways.md)
[6. Gene synteny](./day4/ex16e_data_presentation_Gene_synteny.md)
[7. CAZy heatmaps](./day4/ex16f_OPTIONAL_data_presentation_CAZy_annotations.md) | +
??? calendar-days "Timetable 2023" diff --git a/mkdocs.yml b/mkdocs.yml index f31c869f..246533bb 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -104,7 +104,6 @@ markdown_extensions: custom_checkbox: true - pymdownx.tilde - pymdownx.snippets - - markdown_grid_tables extra_javascript: - javascripts/mathjax.js