Merge pull request #58 from bedapub/dev

docs

README.md

@@ -19,13 +19,7 @@ Another suggestion is to install inside a virtual environment (using `virtualenv
 <summary>Installing splicekit directly from the GitHub repository</summary>
 
 ```
-# move to HOME folder (for example)
-cd ~
-# clone the repository
-git clone [email protected]:bedapub/splicekit.git
-# adjust PYTHONPATH and PATH
-export PYTHONPATH=$PYTHONPATH:~/splicekit
-export PATH=$PATH:~/splicekit/splicekit
+pip install git+https://github.com/bedapub/splicekit.git@main
 ```
 </details>
 
@@ -101,3 +95,13 @@ Easiest is to check [datasets](datasets) examples to see how the above files loo
 * computing edgeR analysis from count tables and producing a results file with direct links to JBrowse2
 * basic motif analysis
 </details>
+
+## Citing and Contact<a name="citation"></a>
+
+If you find **splicekit** useful in your work and research, please cite:
+
+Gregor Rot, Arne Wehling, Roland Schmucki, Nikolaos Berntenis, Jitao David Zhang, Martin Ebeling<br>
+<a href='https://www.biorxiv.org/content/10.1101/2023.05.25.542256v1' target='_biorxiv'>splicekit: a comprehensive toolkit for splicing analysis from short-read RNA-seq</a><br>
+bioRxiv, 2023.05. 25.542256
+
+In case of questions, issues and other ideas, please use the <a href='https://github.com/bedapub/splicekit/issues'>GitHub Issues</a> or write directly to <a href='mailto:[email protected]'>Gregor Rot</a>.

splicekit/__init__.py

@@ -276,4 +276,5 @@ def process(force=False):
     motifs()
     promisc()
     clusterlogfc_process()
+    splicekit.report.process()
     jbrowse2_process(force_samples=force, force_annotation=force)