From 3a327a7a602f7d599555ae3af21d620e0d86a6b2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alba=20Refoyo=20Mart=C3=ADnez?= Date: Wed, 29 May 2024 11:45:39 +0200 Subject: [PATCH 1/2] Update _quarto.yml --- _quarto.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/_quarto.yml b/_quarto.yml index 32070958..ee5a2758 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -14,8 +14,8 @@ website: text: HPC access - href: modules/index.qmd text: Modules - - href: workshop/workshop_june2024.qmd - text: RNAseq Workshop + - href: workshop/workshop_june24.qmd + text: RNAseq Workshop - text: Datasets menu: - href: datasets/datapolicy.qmd From d31ca995f6d95b6204d4f6c890421548ef42ec46 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alba=20Refoyo=20Mart=C3=ADnez?= Date: Mon, 17 Jun 2024 08:59:27 +0200 Subject: [PATCH 2/2] Update workshop_june24.qmd --- workshop/workshop_june24.qmd | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/workshop/workshop_june24.qmd b/workshop/workshop_june24.qmd index c26b2485..875d0b3c 100644 --- a/workshop/workshop_june24.qmd +++ b/workshop/workshop_june24.qmd @@ -49,19 +49,23 @@ Our first choice is to provide all the **training materials, tutorials, and tool Our apps can run on other clusters, simply by pulling a so-called `docker container`. You only need to install `docker` or `singularity` on the cluster. ::: -## Our Sandbox apps +## Transcriptomics apps + +Links to download the material for this workshop: + +- [SLIDES](https://zenodo.org/records/11909973) +- [EVERYTHING ELSE (data, assignments, etc.)](https://zenodo.org/records/10214800) High-Performance Computing (HPC) platforms are essential for large-scale data analysis. Therefore, we will be running our bulk RNA-seq analyses on one of the national HPC platforms. We will guide you through the setup process for using `UCloud`. For more details or to repeat the process on your own, you can also visit [this](https://hds-sandbox.github.io/bulk_RNAseq_course/develop/05a_data_analysis_setup.html) website. - To get started with our transcriptomics app, click [here](https://hds-sandbox.github.io/bulk_RNAseq_course/develop/05a_data_analysis_setup.html) +- To run the nf-core RNAseq pipeline follow the instructions [here](https://hds-sandbox.github.io/bulk_RNAseq_course/develop/04c_preprocessing_setup.html)
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**Transcriptomics Sandbox**: Our sandbox for bulk or single-cell RNA sequencing analysis provides stand-alone visualization tools. In the next update, we will introduce advanced tutorials for more complex single-cell RNA sequencing analysis from some of our supported courses. - - To start setting up the app and review the materials for the various data analysis steps click [here](https://hds-sandbox.github.io/bulk_RNAseq_course/develop/05a_data_analysis_setup.html) - - To run the nf-core RNAseq pipeline follow the instructions [here](https://hds-sandbox.github.io/bulk_RNAseq_course/develop/04c_preprocessing_setup.html)