Update dictionary workflow, docs, and Shiny plot previews

Author: mhurtado13

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: multideconv
 Title: Integrative pipeline for cell type deconvolution from bulk RNAseq using first and second generation methods
 Version: 0.0.1
-Authors@R:c( 
+Authors@R: c( 
     person("Marcelo", "Hurtado", , "marcelo.hurtado@inserm.fr", role = c("aut", "cre"),
            comment = c(ORCID = "0009-0004-6712-0864")),
     person("Vera", "Pancaldi", , "vera.pancaldi@inserm.fr", role = "aut",
@@ -10,43 +10,44 @@ Description: R package that reduces dimensionality and eliminates redundancy thr
 License: GPL (>= 3) + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Depends:
     R (>= 4.3)
 Imports: 
     ADImpute,
+    CellTFusion,
+    DeconRNASeq,
     doParallel,
+    decoupleR,
     dplyr,
     EpiDISH,
-    limSolve,
+    fgsea,
     foreach,
     ggplot2,
     graphics,
     reshape2,
-    ComplexHeatmap,
     factoextra,
     grDevices,
     ggpubr,
     Hmisc (>= 5.2-3),
     immunedeconv (>= 2.1.0),
     matrixStats,
+    msigdbr,
     omnideconv (>= 0.1.0),
     parallel,
+    ppcor,
     glmGamPoi,
     future.apply,
     ggtext,
-    bisque,
     future,
     purrr (>= 1.0.2),
     hdWGCNA (>= 0.4.0),
-    DWLS (>= 0.4),
-    MOMF (>= 0.2),
-    BayesPrism (>= 0.2),
     stats,
     stringr,
     tibble,
     tidyr,
     pcaMethods (>= 1.94),
+    SeuratObject,
     utils,
     grid
 Remotes: 
@@ -69,6 +70,12 @@ Suggests:
     MCPcounter (>= 1.2.0),
     knitr,
     matlib,
+    limSolve,
+    ComplexHeatmap,
+    bisque,
+    DWLS (>= 0.4),
+    MOMF (>= 0.2),
+    BayesPrism (>= 0.2),
     rmarkdown,
     shiny,
     pkgload

NAMESPACE

@@ -1,16 +1,13 @@
 # Generated by roxygen2: do not edit by hand
 
 export(compute.benchmark)
-export(compute.cell.types)
 export(compute.deconvolution)
 export(compute.deconvolution.analysis)
-export(compute.deconvolution.preprocessing)
-export(compute_methods_variable_signature)
-export(compute_sc_deconvolution_methods)
+export(compute_deconvolution_dictionary)
+export(compute_subgroups_pathways)
 export(create_metacells)
 export(create_sc_pseudobulk)
 export(create_sc_signatures)
-export(deconvolution_dictionary)
 export(prepare_multideconv_folds)
 export(replicate_deconvolution_subgroups)
 import(pcaMethods)

R/cell_deconvolution.R

@@ -33,28 +33,37 @@ articles:
 reference:
 - title: Main
   desc: >
-    Compute cell type deconvolution
+    Public user-facing functions
   contents:
   - compute.deconvolution
   - compute.deconvolution.analysis
-  - deconvolution_dictionary
-  - compute.deconvolution.preprocessing
-  - compute_methods_variable_signature
   - replicate_deconvolution_subgroups
+  - compute_deconvolution_dictionary
+  - compute_subgroups_pathways
   - prepare_multideconv_folds
+- title: Benchmarking
+  desc: >
+    Public benchmarking workflow
+  contents:
+  - compute.benchmark
 - title: Single cell functions
   desc: >
-    Single cell data manipulation for deconvolution
+    Public single-cell utilities
   contents:
   - create_metacells
   - create_sc_pseudobulk
   - create_sc_signatures
-  - compute_sc_deconvolution_methods
-  - compute.benchmark
 - title: Utils
   desc: >
     Internal use (not exported functions)
   contents:
+  - standardize_celltype_colnames
+  - compute.deconvolution.preprocessing
+  - compute_methods_variable_signature
+  - compute_sc_deconvolution_methods
+  - deconvolution_dictionary
+  - compute_data_driven_rank
+  - create_gsea_signature
   - computeCBSX
   - computeCBSX_parallel
   - computeDWLS
@@ -68,11 +77,11 @@ reference:
   - computeXCell
   - compute_subgroups
   - compute.cell.types
+  - corr_subgroups
   - remove_subgroups
   - remove_low_variance
   - find.maximum.iteration
   - removeCorrelatedFeatures
-  - correlation
 - title: Package Data
   desc: >
     Example data