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