rnadeseq

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Prepare release 2.3

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## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested,...

WackerO

Release 2.3

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## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested,...

WackerO

### Description of feature As requested here: https://github.com/qbic-pipelines/rnadeseq/issues/224, reduce pathway heatmaps to only display samples from the current contrast.

WackerO

Use --relevel parameter for PCA plotting

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### Description of feature The `--relevel `parameter in rnadeseq is primarily there for modeling in DE analysis ( i assume/recall). I just noticed that it has no influence on the...

qbicStefanC

Improve documentation: Troubleshooting

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### Description of feature Suggestion: Please add a troubleshooting section with common error messages that helps users to quickly understand what they're missing to get the pipeline running. I suggest...

SusiJo

### Description of the bug When running rnadeseq with a contrast list that contains a factor not described in the design file, the following error is thrown: Error in cleanContrast(object,...

WackerO

### Description of the bug Check if transcript ID works for all relevant gtf files ### Command used and terminal output _No response_ ### Relevant files _No response_ ### System...

WackerO

Fix contrast pairs

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This ensures that the contrast pair file is correctly read. Also, it adds clearer error messages if the contrasts are not correctly defined. ## PR checklist - [ ] This...

WackerO

## PR checklist Fixes the ggsave error when many genes are DE. With many genes being DE, one might need to adapt resource requirements. Therefore, usage docs were updated to...

SusiJo

## PR checklist Only takes effect if a `gtf` file is provided as input and if the field `gene_biotype` is available in the attributes of the `gtf` file. - [x]...

SusiJo