KU Workshop 2024. Vampirium release. Hotfix

This is the release version used in the University of Copenhagen (KU) workshop on bulk RNAseq analysis for 2024. It includes theory and materials to run a bulk RNAseq analysis starting from the preprocessing reads, including some experimental considerations and RNAseq theory.

This workshop is based on the materials developed by members of the teaching team at the Harvard Chan Bioinformatics Core (HBC), a collection of modified tutorials from the DESeq2, R language vignettes and the nf-core pipeline for bulk RNAseq.

In this release, we have moved all supplementary material (data, assignments, slides, etc). to the zenodo repository (10.5281/zenodo.7116370). We have also updated the paths of the files so they are not broken when using UCloud.
In addition, some bugs from the first vampirium version (4.0.1) have been fixed.

KU Workshop 2024. First Vampirium release

This is the release version used in the University of Copenhagen (KU) workshop on bulk RNAseq analysis for 2024. It includes theory and materials to run a bulk RNAseq analysis starting from the preprocessing reads, including some experimental considerations and RNAseq theory.

This workshop is based on the materials developed by members of the teaching team at the Harvard Chan Bioinformatics Core (HBC), a collection of modified tutorials from the DESeq2, R language vignettes and the nf-core pipeline for bulk RNAseq.

In this release, we have moved all supplementary material (data, assignments, slides, etc). to the zenodo repository(10.5281/zenodo.7116370). We have also updated the paths of the files so they are not broken when using UCloud.

Note: This is the first vampirium setup

KU Workshop 2023 June. Final version before vampirium setup

This is the release version used in the University of Copenhagen (KU) workshop on bulk RNAseq analysis in June 2023. It includes theory and materials to run a bulk RNAseq analysis starting from the preprocessing reads, including some experimental considerations and RNAseq theory.

This workshop is based on the materials developed by members of the teaching team at the Harvard Chan Bioinformatics Core (HBC), a collection of modified tutorials from the DESeq2, R language vignettes and the nf-core pipeline for bulk RNAseq.

In this release, we have moved all supplementary material (tdata, assignments, slides, etc). to the zenodo repository(10.5281/zenodo.7802718). We have also updated the paths of the files so they are not broken when using UCloud.

Note: this is the final version before the vampirium setup

KU Workshop 2023 June. GLM hotfix

This is the release version used in the University of Copenhagen (KU) workshop on bulk RNAseq analysis in June 2023. It includes theory and materials to run a bulk RNAseq analysis starting from the preprocessing reads, including some experimental considerations and RNAseq theory.

This workshop is based on the materials developed by members of the teaching team at the Harvard Chan Bioinformatics Core (HBC), a collection of modified tutorials from the DESeq2, R language vignettes and the nf-core pipeline for bulk RNAseq.

In this release, we have moved all supplementary material (tdata, assignments, slides, etc). to the zenodo repository(10.5281/zenodo.7802718). We have also updated the paths of the files so they are not broken when using UCloud.

Note: This version has corrected info on the LFC calculations.

KU Workshop 2023 June. Hotfix

This is the release version used in the University of Copenhagen (KU) workshop on bulk RNAseq analysis in June 2023. It includes theory and materials to run a bulk RNAseq analysis starting from the preprocessing reads, including some experimental considerations and RNAseq theory.

This workshop is based on the materials developed by members of the teaching team at the Harvard Chan Bioinformatics Core (HBC), a collection of modified tutorials from the DESeq2, R language vignettes and the nf-core pipeline for bulk RNAseq.

In this release, we have moved all supplementary material (tdata, assignments, slides, etc). to the zenodo repository(10.5281/zenodo.7802718). We have also updated the paths of the files so they are not broken when using UCloud.

Note: this version is a hotfix for dplyr packages filter and select functions and also some path corrections of the summarised workflow notebook.

KU Workshop 2023 June

This is the release version used in the University of Copenhagen (KU) workshop on bulk RNAseq analysis in June 2023. It includes theory and materials to run a bulk RNAseq analysis starting from the preprocessing reads, including some experimental considerations and RNAseq theory.

This workshop is based on the materials developed by members of the teaching team at the Harvard Chan Bioinformatics Core (HBC), a collection of modified tutorials from the DESeq2, R language vignettes and the nf-core pipeline for bulk RNAseq.

In this release, we have moved all supplementary material (tdata, assignments, slides, etc). to the zenodo repository(10.5281/zenodo.7802718). We have also updated the paths of the files so they are not broken when using UCloud.

KU Workshop 2023 January

This is the release version used in the University of Copenhagen (KU) workshop on bulk RNAseq analysis in January 2023. It includes theory and materials to run a bulk RNAseq analysis starting from the preprocessing reads, including some experimental considerations and RNAseq theory.

This workshop is based on the materials developed by members of the teaching team at the Harvard Chan Bioinformatics Core (HBC), a collection of modified tutorials from the DESeq2, R language vignettes and the nf-core pipeline for bulk RNAseq.

Webpage has been moved to branch webpage.

KU Workshop 2023 January

This is the release version used in the University of Copenhagen (KU) workshop on bulk RNAseq analysis in January 2023. It includes theory and materials to run a bulk RNAseq analysis starting from the preprocessing reads, including some experimental considerations and RNAseq theory.

Materials were taken and adapted from Harvard Chan Bioinformatics Core (HBC), the DESEQ2
tutorial and the clusterProfiler book.

The webpage is outdated and still relates to the previous release of the course. We are currently working on updating it!

KU Workshop 2022 August

This is the release version used in the University of Copenhagen (KU) workshop on bulk RNAseq analysis in August 2022. It includes theory and materials to run a bulk RNAseq analysis starting from the count matrix, including some experimental considerations and read-processing theory.

Materials were taken and adapted from Harvard Chan Bioinformatics Core (HBC), the DESEQ2
tutorial and the clusterProfiler book.

This release is the same as v1.0 but linked to a zenodo DOI

KU Workshop 2022 August

This is the release version used in the University of Copenhagen (KU) workshop on bulk RNAseq analysis in August 2022. It includes theory and materials to run a bulk RNAseq analysis starting from the count matrix, including some experimental considerations and read-processing theory.

Materials were taken and adapted from Harvard Chan Bioinformatics Core (HBC), the DESEQ2
tutorial and the clusterProfiler book.