cell type specific grns for portia and grnboost2

scripts/sbatch/batch_grnboost2.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+#SBATCH --time=12:00:00
+#SBATCH --job-name=grnboost2
+#SBATCH --output=logs/%j.out
+#SBATCH --error=logs/%j.err
+#SBATCH --mail-type=END
+#SBATCH [email protected]
+#SBATCH --cpus-per-task=20
+#SBATCH --mem=64G 
+
+singularity exec ../../images/scenic python src/methods/single_omics/grnboost2/script.py 

scripts/sbatch/batch_portia.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+#SBATCH --time=2:00:00
+#SBATCH --job-name=portia
+#SBATCH --output=logs/%j.out
+#SBATCH --error=logs/%j.err
+#SBATCH --mail-type=END
+#SBATCH [email protected]
+#SBATCH --cpus-per-task=20
+#SBATCH --mem=120G 
+
+singularity exec ../../images/portia python src/methods/single_omics/portia/script.py 

scripts/sbatch/batch_scenicplus.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+#SBATCH --time=2:00:00
+#SBATCH --job-name=scenicplus
+#SBATCH --output=logs/%j.out
+#SBATCH --error=logs/%j.err
+#SBATCH --mail-type=END
+#SBATCH [email protected]
+#SBATCH --cpus-per-task=20
+#SBATCH --mem=64G 
+
+singularity exec ../../images/scenicplus_old python src/methods/multi_omics/scenicplus/script.py 

src/control_methods/baseline_corr/script.py

@@ -9,14 +9,15 @@
 
 ## VIASH START
 par = {
-    'multiomics_rna': 'resources/grn-benchmark/multiomics_rna.h5ad',
+    'multiomics_rna': 'resources/grn-benchmark/perturbation_data.h5ad',
     'tf_all': 'resources/prior/tf_all.csv',
     'causal': True,
     'metacell': False,
     'cell_type_specific': True,
     'impute': False,
     'max_n_links': 50000,
-    'corr_method': 'pearson'
+    'corr_method': 'pearson',
+    'prediction': 'resources/grn_models/positive_control.csv'
 }
 ## VIASH END
 print(par)