Changed to decoupler for pseudobulking (#141)

jupyter-book/conditions/differential_gene_expression.bib

@@ -551,4 +551,21 @@ @Article{de:Hao2021
   year = {2021},
   doi = {10.1016/j.cell.2021.04.048},
   url = {https://doi.org/10.1016/j.cell.2021.04.048},
-}
+}
+
+@article{de:Badia-i-Mompel2022,
+    author = {Badia-i-Mompel, Pau and Vélez Santiago, Jesús and Braunger, Jana and Geiss, Celina and Dimitrov, Daniel and Müller-Dott, Sophia and Taus, Petr and Dugourd, Aurelien and Holland, Christian H and Ramirez Flores, Ricardo O and Saez-Rodriguez, Julio},
+    title = "{decoupleR: ensemble of computational methods to infer biological activities from omics data}",
+    journal = {Bioinformatics Advances},
+    volume = {2},
+    number = {1},
+    year = {2022},
+    month = {03},
+    issn = {2635-0041},
+    doi = {10.1093/bioadv/vbac016},
+    url = {https://doi.org/10.1093/bioadv/vbac016},
+    note = {vbac016},
+}
+
+
+

jupyter-book/conditions/differential_gene_expression_environment.yml

@@ -11,9 +11,10 @@ dependencies:
   - bioconda::bioconductor-edger=3.40.0
   - bioconda::bioconductor-singlecellexperiment=1.20.0
   - conda-forge::r-lme4
-  - conda-forge::notebook
+  - conda-forge::jupyterlab
   - conda-forge::rpy2=3.5.6
   - bioconda::anndata2ri=1.1
   - conda-forge::pip
   - pip:
       - sc-toolbox
+      - decoupler