update pixi

Author: RibaA

pixi.toml

@@ -1,9 +1,9 @@
 [workspace]
 name = "spatial-analysis-framework-hnscc"
 authors = [
-    "Farnoosh Abbas Aghababazadeh <bhklab.farnooshabbasaghababazadeh@gmail.com>"
+    "Farnoosh Abbas Aghababazadeh <farnoosh.abbasaghababazadeh@uhn.ca>, Gregoire Marret <gregoire.marret@uhn.ca>, Jinsu An <jinsu.an@ucalgary.ca>"
 ]
-description = "A Spatial Analysis Framework for Head and Neck Squamous Cell Carcinoma"
+description = "This repository contains computational workflows for analyzing spatial transcriptomics data from recurrent/metastatic head and neck squamous cell carcinoma (RM-HNSCC). The analyses characterize spatial tumor–immune–stromal organization, infer cell–cell communication, and derive spatially informed gene expression signatures that predict response to immune checkpoint blockade across cancer types."
 license = "MIT"
 channels = ["conda-forge", "bioconda"]
 platforms = ["osx-arm64", "linux-64", "win-64", "osx-64"]
@@ -29,9 +29,34 @@ ipykernel = "*"
 jupyterlab = "*"
 pip = "*"
 
+# R and core packages
+r-base = ">=4.3,<4.4"
+r-devtools = "*"
+r-remotes = "*"
+
+# CRAN packages with versions (when available via conda)
+r-hmisc = "==5.1_3"
+r-circlize = "==0.4.16"
+r-enrichr = "==3.2"
+r-forestplot = "==3.1.3"
+r-meta = "==7.0_0"
+
+[tasks.postInstall]
+cmd = [
+  "Rscript -e \"if (!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager')\"",
+  "Rscript -e \"BiocManager::install('GSVA')\"",
+  "Rscript -e \"BiocManager::install('MultiAssayExperiment')\"",
+  "Rscript -e \"BiocManager::install('survcomp')\"",
+  "Rscript -e \"BiocManager::install('singscore')\"",
+  "Rscript -e \"BiocManager::install('ComplexHeatmap')\"",
+  "Rscript -e \"remotes::install_github('bhklab/PredictioR', ref = '46a2708fc7455a4cd064334b3de2407c7c82db73')\""
+]
+description = "Install Bioconductor and GitHub R packages"
+
 [pypi-dependencies]
 damply = ">=0.10.0, <0.11"
 
+
 [tasks]
 example_script = {cmd="python $SCRIPTS/example_script.py", description="Run an example script"}