From 813c46e15fbd95aebcb09e25341c7db19f30c082 Mon Sep 17 00:00:00 2001
From: SciLiciumTheo <101104633+SciLiciumTheo@users.noreply.github.com>
Date: Wed, 2 Apr 2025 16:34:34 +0200
Subject: [PATCH 1/5] Add new methods to deconvBench

---
 pipeline/bin/computeSignaturesNF.R  | 10 +++++++---
 pipeline/optimal_normalizations.csv | 22 +++++++++++++---------
 2 files changed, 20 insertions(+), 12 deletions(-)

diff --git a/pipeline/bin/computeSignaturesNF.R b/pipeline/bin/computeSignaturesNF.R
index b456aa5..948ee26 100755
--- a/pipeline/bin/computeSignaturesNF.R
+++ b/pipeline/bin/computeSignaturesNF.R
@@ -38,9 +38,13 @@ source(paste0(baseDir, '/bin/utils.R'))
 method_normalizations <- read.table(paste0(baseDir, '/optimal_normalizations.csv'), sep = ',', header = TRUE)
 
 # find method-specific normalizations for sc and bulk
-sc_norm <- method_normalizations[method_normalizations$method == method, 2]
-bulk_norm <- method_normalizations[method_normalizations$method == method, 3]
-print(paste0('Method: ', method, '; sc-norm: ', sc_norm, '; bulk-norm: ', bulk_norm))
+if(method %in% method_normalizations$method){
+    sc_norm <- method_normalizations[method_normalizations$method == method, 2]
+    bulk_norm <- method_normalizations[method_normalizations$method == method, 3]
+    print(paste0('Method: ', method, '; sc-norm: ', sc_norm, '; bulk-norm: ', bulk_norm))
+} else {
+    stop(paste0('Method ', method, ' is not currently supported. Exiting.')) 
+}
 
 # check if preprocessing has been performed
 if(args$run_preprocessing == 'true'){
diff --git a/pipeline/optimal_normalizations.csv b/pipeline/optimal_normalizations.csv
index f17c602..349894a 100644
--- a/pipeline/optimal_normalizations.csv
+++ b/pipeline/optimal_normalizations.csv
@@ -1,10 +1,14 @@
-method,sc_norm,bulk_norm
-autogenes,cpm,tpm
-bayesprism,counts,counts
-bisque,counts,counts
-cibersortx,cpm,tpm
-dwls,counts,tpm
-music,counts,tpm
-scaden,counts,tpm
-scdc,counts,tpm
+method,sc_norm,bulk_norm
+autogenes,cpm,tpm
+bayesprism,counts,counts
+bisque,counts,counts
+bseqsc,counts,tpm
+cdseq,counts,counts
+cibersortx,cpm,tpm
+cpm,counts,counts
+dwls,counts,tpm
+momf,counts,counts
+music,counts,tpm
+scaden,counts,tpm
+scdc,counts,tpm
 rectangle,counts,tpm
\ No newline at end of file

From d6bc7d537831b0a72662f65f8bd4aebdf45d15b4 Mon Sep 17 00:00:00 2001
From: SciLiciumTheo <101104633+SciLiciumTheo@users.noreply.github.com>
Date: Thu, 3 Apr 2025 11:22:54 +0200
Subject: [PATCH 2/5] Add cpm as deconvolution method

---
 pipeline/bin/utils.R | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/pipeline/bin/utils.R b/pipeline/bin/utils.R
index ee007de..52b5f83 100755
--- a/pipeline/bin/utils.R
+++ b/pipeline/bin/utils.R
@@ -257,7 +257,7 @@ signature_workflow_general <- function(sc_matrix, annotations, annotation_catego
       verbose = TRUE
     )
 
-  }else if (method %in% c('autogenes', 'bayesprism', 'bisque', 'music')){
+  }else if (method %in% c('autogenes', 'bayesprism', 'bisque', 'cdseq', 'cpm', 'music')){
     signature <- NULL
       
   } else {
@@ -365,6 +365,15 @@ deconvolution_workflow_general <- function(sc_matrix, annotations, annotation_ca
     unlink(cx_input, recursive=TRUE)
     unlink(cx_output, recursive=TRUE)
     
+  } else if (method=="cpm"){
+
+    deconvolution <- omnideconv::deconvolute_cpm(
+      bulk_gene_expression = bulk_matrix, 
+      single_cell_object = sc_matrix, 
+      cell_type_annotations = annotations,
+      verbose = TRUE,
+    )$cellTypePredictions
+    
   } else if(method=="dwls") {
     
     deconvolution <- omnideconv::deconvolute_dwls(

From 721b1f7549b97f9387b754f938b20b51323f6ba0 Mon Sep 17 00:00:00 2001
From: SciLiciumTheo <101104633+SciLiciumTheo@users.noreply.github.com>
Date: Thu, 3 Apr 2025 15:28:50 +0200
Subject: [PATCH 3/5] Add support for CDseq

By default, the CDseq call will use the reduce-recover strategy with 10 blocks of 1k genes to speed-up computations.
See Kang et al. (BMC bioinformatics, 2021) publication (https://doi.org/10.1186/s12859-021-04186-5)
---
 pipeline/bin/utils.R | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/pipeline/bin/utils.R b/pipeline/bin/utils.R
index 52b5f83..a662a21 100755
--- a/pipeline/bin/utils.R
+++ b/pipeline/bin/utils.R
@@ -328,6 +328,21 @@ deconvolution_workflow_general <- function(sc_matrix, annotations, annotation_ca
       batch_ids = sc_batch,
       verbose = TRUE,
     )$bulk.props)
+
+  } else if (method=="cdseq"){
+
+    deconvolution_cdseq <- omnideconv::deconvolute_cdseq(
+      bulk_gene_expression = bulk_matrix, 
+      single_cell_object = sc_matrix, 
+      cell_type_annotations = annotations,
+      batch_ids = sc_batch,
+      block_number=10,
+      gene_subset_size=1000,
+      verbose = TRUE,
+    )
+    
+    deconvolution <- t(deconvolution_cdseq$cdseq_prop_merged)
+    print(deconvolution)
     
   } else if (method=="cibersortx"){
 

From cca7780a9058756851b750030c20eba430368637 Mon Sep 17 00:00:00 2001
From: SciLiciumTheo <101104633+SciLiciumTheo@users.noreply.github.com>
Date: Thu, 3 Apr 2025 16:59:29 +0200
Subject: [PATCH 4/5] Adding momf to available tools

---
 pipeline/bin/utils.R | 24 +++++++++++++++++++++---
 1 file changed, 21 insertions(+), 3 deletions(-)

diff --git a/pipeline/bin/utils.R b/pipeline/bin/utils.R
index a662a21..076f1ef 100755
--- a/pipeline/bin/utils.R
+++ b/pipeline/bin/utils.R
@@ -238,6 +238,14 @@ signature_workflow_general <- function(sc_matrix, annotations, annotation_catego
       verbose = TRUE
     )$basis
     
+  } else if (method == "momf") {
+    
+    signature <- omnideconv::build_model_momf(
+      sc_matrix,
+      annotations,
+      bulk_matrix
+    )
+    
   } else if(method == "scaden"){
     unlink(tmp_dir_path, recursive=TRUE)
     if(!dir.exists(paste0(tmp_dir_path))){
@@ -257,7 +265,7 @@ signature_workflow_general <- function(sc_matrix, annotations, annotation_catego
       verbose = TRUE
     )
 
-  }else if (method %in% c('autogenes', 'bayesprism', 'bisque', 'cdseq', 'cpm', 'music')){
+  } else if (method %in% c('autogenes', 'bayesprism', 'bisque', 'cdseq', 'cpm', 'music')){
     signature <- NULL
       
   } else {
@@ -420,8 +428,18 @@ deconvolution_workflow_general <- function(sc_matrix, annotations, annotation_ca
     #)
     print(deconvolution)
 
-  } else if (method == "music"){
-    deconvolution <- omnideconv::deconvolute_music(
+  } else if (method == "momf"){
+    deconvolution_momf <- omnideconv::deconvolute_momf(
+          bulk_matrix,
+          signature, 
+          sc_matrix, 
+          verbose = TRUE,
+        )
+    
+    deconvolution <- deconvolution_momf$cell.prop
+
+  }  else if (method == "music"){
+    deconvolution <- omnideconv::deconvolute_momf(
       bulk_gene_expression = bulk_matrix, 
       single_cell_object = sc_matrix, 
       cell_type_annotations = annotations,

From 872987c39ba27aa6b54aa9d57e3295bc975a0945 Mon Sep 17 00:00:00 2001
From: SciLiciumTheo <101104633+SciLiciumTheo@users.noreply.github.com>
Date: Thu, 3 Apr 2025 17:27:59 +0200
Subject: [PATCH 5/5] Drop bseqsc from config file

---
 pipeline/optimal_normalizations.csv | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pipeline/optimal_normalizations.csv b/pipeline/optimal_normalizations.csv
index 349894a..89da674 100644
--- a/pipeline/optimal_normalizations.csv
+++ b/pipeline/optimal_normalizations.csv
@@ -2,7 +2,6 @@ method,sc_norm,bulk_norm
 autogenes,cpm,tpm
 bayesprism,counts,counts
 bisque,counts,counts
-bseqsc,counts,tpm
 cdseq,counts,counts
 cibersortx,cpm,tpm
 cpm,counts,counts