add CITATION file

CITATION.cff

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+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: >-
+ scCRISPR-seq Perturbation Analysis Workflow using Seurat's
+ Mixscape
+message: >-
+ If you use this software, please cite it using the
+ metadata from this file.
+type: software
+authors:
+ - given-names: Stephan
+ family-names: Reichl
+ orcid: 'https://orcid.org/0000-0001-8555-7198'
+ affiliation: CeMM Research Center for Molecular Medicine
+ - given-names: Christoph
+ family-names: Bock
+ orcid: 'https://orcid.org/0000-0001-6091-3088'
+ affiliation: CeMM Research Center for Molecular Medicine
+repository-code: 'https://github.com/epigen/mixscape_seurat'
+url: 'https://epigen.github.io/mixscape_seurat/'
+abstract: >-
+ A Snakemake workflow for performing perturbation analyses
+ of pooled (multimodal) CRISPR screens with sc/snRNA-seq
+ read-out (scCRISPR-seq) using the R package Seurat's
+ method Mixscape.
+keywords:
+ - scCRISPR-seq
+ - Perturbation Analysis
+ - Bioinformatics
+ - Workflow
+ - Snakemake
+license: MIT

README.md

@@ -1,6 +1,8 @@
 # scCRISPR-seq Perturbation Analysis Snakemake Workflow powered by Seurat's Mixscape
 A [Snakemake](https://snakemake.readthedocs.io/en/stable/) workflow for performing perturbation analyses of pooled (multimodal) CRISPR screens with sc/snRNA-seq read-out (scCRISPR-seq) powered by the R package [Seurat's](https://satijalab.org/seurat/index.html) method [Mixscape](https://satijalab.org/seurat/articles/mixscape_vignette.html).
 
+This workflow adheres to the module specifications of [MR.PARETO](https://github.com/epigen/mr.pareto), an effort to augment research by modularizing (biomedical) data science. For more details and modules check out the project's repository.
+
 **If you use this workflow in a publication, don't forget to give credits to the authors by citing the URL of this (original) repository (and its DOI, see Zenodo badge above -> coming soon).**
 
 ![Workflow Rulegraph](./workflow/dags/rulegraph.svg)
@@ -15,17 +17,22 @@ Table of contents
  * [Configuration](#configuration)
  * [Example](#example)
  * [Links](#links)
+ * [Publications](#publications)
 
 # Authors
 - [Stephan Reichl](https://github.com/sreichl)
+- [Christoph Bock](https://github.com/chrbock)
 
 
 # Software
 This project wouldn't be possible without the following software and it's dependencies:
 
 | Software | Reference (DOI) |
 | :------------: | :-----------------------------------------------: |
+| ggplot2 | https://ggplot2.tidyverse.org/ |
 | Mixscape | https://doi.org/10.1038/s41588-021-00778-2 |
+| mixtools | https://CRAN.R-project.org/package=mixtools |
+| patchwork | https://CRAN.R-project.org/package=patchwork |
 | Seurat | https://doi.org/10.1016/j.cell.2021.04.048 |
 | Snakemake | https://doi.org/10.12688/f1000research.29032.2 |
 
@@ -70,3 +77,7 @@ Detailed specifications can be found here [./config/README.md](./config/README.m
 - [GitHub Page](https://epigen.github.io/mixscape_seurat/)
 - [Zenodo Repository (coming soon)]()
 - [Snakemake Workflow Catalog Entry](https://snakemake.github.io/snakemake-workflow-catalog?usage=epigen/mixscape_seurat)
+
+# Publications
+The following publications successfully used this module for their analyses.
+- ...