Code and data for "Bordetella adenylate cyclase toxin elicits chromatin remodeling and transcriptional reprogramming that blocks differentiation of monocytes into macrophages"

<p># Code and data for &quot;Bordetella adenylate cyclase toxin elicits chromatin remodeling and transcriptional reprogramming that blocks differentiation of monocytes into macrophages&quot;</p> <p><br> - `pipeline` contains scripts for processing raw reads with `nf-core/rnaseq` Nextflow pipeline<br> &nbsp; - `setup_conda.sh` sets up a conda environment for Nextflow<br> &nbsp; - `samplesheet.csv` describes the samples<br> &nbsp; - `rna-seq-nextflow.sh` runs the analysis<br> - `data` contains the quantifications by Salmon from the pipeline and data for the CRE motif (see `analysis.Rmd` for more details)<br> - `analysis.Rmd` an R notebook containing a code to reproduce conclusions and figures in the paper and additional comments.</p> <p>The R environment (all packages) is reproducibly reconstructed via `renv` - run `renv::restore()` after loading the project.</p> <p>The generated figures and tables are stored in the `outputs` directory.</p> <p>&nbsp;</p>