README.md

nf-deseq2

Running the workflow:

RELEASE=1.0.0
PROFILE=local
nextflow run mpg-age-bioinformatics/nf-deseq2 -r ${RELEASE} -params-file params.json -entry images -profile ${PROFILE} && \
nextflow run mpg-age-bioinformatics/nf-deseq2 -r ${RELEASE} -params-file params.json -entry preprocess -profile ${PROFILE} && \
nextflow run mpg-age-bioinformatics/nf-deseq2 -r ${RELEASE} -params-file params.json -entry pairwise -profile ${PROFILE} && \
nextflow run mpg-age-bioinformatics/nf-deseq2 -r ${RELEASE} -params-file params.json -entry annotate -profile ${PROFILE} && \
nextflow run mpg-age-bioinformatics/nf-deseq2 -r ${RELEASE} -params-file params.json -entry david -profile ${PROFILE} && \
nextflow run mpg-age-bioinformatics/nf-deseq2 -r ${RELEASE} -params-file params.json -entry topgo -profile ${PROFILE} && \
nextflow run mpg-age-bioinformatics/nf-deseq2 -r ${RELEASE} -params-file params.json -entry cellplots -profile ${PROFILE} && \
nextflow run mpg-age-bioinformatics/nf-deseq2 -r ${RELEASE} -params-file params.json -entry rcistarget -profile ${PROFILE} && \
nextflow run mpg-age-bioinformatics/nf-deseq2 -r ${RELEASE} -params-file params.json -entry qc -profile ${PROFILE} && \
nextflow run mpg-age-bioinformatics/nf-deseq2 -r ${RELEASE} -params-file params.json -entry string_cytoscape -profile ${PROFILE}

---

Contributing

Make a commit, check the last tag, add a new one, push it and make a release:

git add -A . && git commit -m "<message>" && git push
git describe --abbrev=0 --tags
git tag -e -a <tag> HEAD
git push origin --tags
gh release create <tag> 

---

Material and Methods

Differential gene expression

After normalization of read counts by making use of the standard median-ratio for estimation of size factors, pair-wise differential gene expression was performed using DESeq2/1.24.0

After removal of genes with less then 10 overall reads log2 fold changes were shrank using approximate posterior estimation for GLM coefficients.