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Merged
WackerO merged 4 commits into from
Dec 21, 2022
Merged

Add nf-core citation #175

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15695fc
Added nf-core citation
WackerO Dec 19, 2022
05da634
Updated changelog
WackerO Dec 20, 2022
5076f98
Fixed left-padding
WackerO Dec 21, 2022
1d8cff4
Merge branch 'dev' of https://github.com/qbic-pipelines/rnadeseq into…
WackerO Dec 21, 2022
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Added

- [#175](https://github.com/qbic-pipelines/rnadeseq/pull/175) Added nf-core citation to report
- [#173](https://github.com/qbic-pipelines/rnadeseq/pull/173) Added GMT file to testdata dir to test #172
- [#172](https://github.com/qbic-pipelines/rnadeseq/pull/172) Added option to provide custom gost GMT, for online gost, GMT is downloaded
- [#151](https://github.com/qbic-pipelines/rnadeseq/pull/151) Added session info to report
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2 changes: 1 addition & 1 deletion assets/RNAseq_report.Rmd
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Expand Up @@ -1921,7 +1921,7 @@ An aggregation of the quality control for the RNAseq analysis was performed with

## Differential gene expression analysis

The differential expression analysis was performed by the use of the `rnadeseq `r as.character(params$revision)`` pipeline [^5]. For differential expression analysis, the raw read count table resulting from `featureCounts` was processed with the R package `DESeq2 v`r packageVersion("DESeq2")`` [@love2014differential].
The differential expression analysis was performed by the use of the `rnadeseq `r as.character(params$revision)`` pipeline [^5], which was written using the nf-core template [@ewels2020nf]. For differential expression analysis, the raw read count table resulting from `featureCounts` was processed with the R package `DESeq2 v`r packageVersion("DESeq2")`` [@love2014differential].

```{r conditional_pathway2, echo=FALSE, results='asis', eval=params$pathway_analysis}
version_gprofiler2 = packageVersion("gprofiler2")
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13 changes: 10 additions & 3 deletions assets/references.bibtex
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Expand Up @@ -187,6 +187,13 @@ journal="BMC Bioinformatics",
year={2012},
publisher={Cold Spring Harbor Lab}
}



@article{ewels2020nf,
title={The nf-core framework for community-curated bioinformatics pipelines},
author={Ewels, Philip A and Peltzer, Alexander and Fillinger, Sven and Patel, Harshil and Alneberg, Johannes and Wilm, Andreas and Garcia, Maxime Ulysse and Di Tommaso, Paolo and Nahnsen, Sven},
journal={Nature biotechnology},
volume={38},
number={3},
pages={276--278},
year={2020},
publisher={Nature Publishing Group}
}
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