From f1207f891a2798910f9e7d616aba91f40b47d316 Mon Sep 17 00:00:00 2001 From: A Wokaty Date: Wed, 29 Oct 2025 11:38:57 -0400 Subject: [PATCH 1/7] bump x.y.z version to even y prior to creation of RELEASE_3_22 branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 867b8a6..06c16e7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: iModMix Title: Integrative Modules for Multi-Omics Data -Version: 0.99.3 +Version: 1.0.0 Authors@R: c( person(given = "Isis", family = "Narvaez-Bandera", From 096c0d65f7e160c5821fa557ff87fcf610122c5f Mon Sep 17 00:00:00 2001 From: A Wokaty Date: Wed, 29 Oct 2025 11:38:57 -0400 Subject: [PATCH 2/7] bump x.y.z version to odd y following creation of RELEASE_3_22 branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 06c16e7..a984bf7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: iModMix Title: Integrative Modules for Multi-Omics Data -Version: 1.0.0 +Version: 1.1.0 Authors@R: c( person(given = "Isis", family = "Narvaez-Bandera", From 934d0710234824fe7aa7cceb3e3a1cf05f1567f9 Mon Sep 17 00:00:00 2001 From: IsisNarvaez Date: Mon, 8 Dec 2025 12:15:52 -0500 Subject: [PATCH 3/7] Data2 to data and increase memory --- R/mod_module1.R | 12 ++++++------ R/run_app.R | 3 ++- 2 files changed, 8 insertions(+), 7 deletions(-) diff --git a/R/mod_module1.R b/R/mod_module1.R index 3e5f06d..b46c588 100644 --- a/R/mod_module1.R +++ b/R/mod_module1.R @@ -1674,9 +1674,9 @@ mod_module1_server <- function(id){ ###### Data2 # Data Input - observeEvent(input$Data2, { - req(input$Data2) - filedata_value <- read.csv(input$Data2$datapath) + observeEvent(input$data2, { + req(input$data2) + filedata_value <- read.csv(input$data2$datapath) Prot_exp(filedata_value) }) @@ -2233,9 +2233,9 @@ mod_module1_server <- function(id){ ####### Data3 # Data Input - observeEvent(input$Data3, { - req(input$Data3) - filedata_value <- read.csv(input$Data3$datapath) + observeEvent(input$data3, { + req(input$data3) + filedata_value <- read.csv(input$data3$datapath) Gene_exp(filedata_value) }) diff --git a/R/run_app.R b/R/run_app.R index e9c99c8..8bfd769 100644 --- a/R/run_app.R +++ b/R/run_app.R @@ -16,7 +16,8 @@ run_app <- function( uiPattern = "/", ... ) -{ # --- START: Inicialización de iModMixData --- +{ options(shiny.maxRequestSize = 1000*1024^2) # 100 MB + # --- START: Inicialización de iModMixData --- eh_cache <- tools::R_user_dir("ExperimentHub", "cache") if (!dir.exists(eh_cache)) dir.create(eh_cache, recursive = TRUE) eh <- ExperimentHub::ExperimentHub() From d8af76d533895d08350ba8e445e915deb581c1ff Mon Sep 17 00:00:00 2001 From: IsisNarvaez Date: Fri, 6 Mar 2026 11:33:49 -0500 Subject: [PATCH 4/7] Update vignette example data section with Zenodo DOI link --- DESCRIPTION | 2 +- inst/app/www/GetStarted.Rmd | 9 +++++++-- inst/app/www/GetStarted.html | 17 ++++++++++++----- 3 files changed, 20 insertions(+), 8 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index a984bf7..8a391e3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: iModMix Title: Integrative Modules for Multi-Omics Data -Version: 1.1.0 +Version: 1.1.1 Authors@R: c( person(given = "Isis", family = "Narvaez-Bandera", diff --git a/inst/app/www/GetStarted.Rmd b/inst/app/www/GetStarted.Rmd index 81897b2..d0b7a5c 100644 --- a/inst/app/www/GetStarted.Rmd +++ b/inst/app/www/GetStarted.Rmd @@ -64,9 +64,14 @@ To ensure your data is ready for analysis, please follow these guidelines: - Web-based Tools for ID Conversion: If you need to convert identifiers, consider using web-based tools like the Uniprot batch conversion tool for genes/proteins or DAVID for genes. - Ensure that the sample IDs in your metadata file match those in your omics data files. If there are discrepancies, an error will occur. Make sure all samples are labeled correctly with no extra or missing samples. -## Example data. +## Example data -Two case studies are available to help you get started with iModMix. You can use this data to run the application and explore its features. +We provide ten multi-omic datasets (transcriptomics and metabolomics) to further illustrate iModMix’s capabilities. These datasets (Benedetti et al. 2023) have been formatted to meet iModMix specifications, with variable columns labeled as “Feature_ID” and sample columns labeled as “Samples”. + +These datasets are readily accessible for download on Zenodo: +[https://doi.org/10.5281/zenodo.13988161](https://doi.org/10.5281/zenodo.13988161) + +Furthermore, two case studies are available to help you get started with iModMix. You can use this data to run the application and explore its features. **Case Study 1.** Clear cell renal cell carcinoma (ccRCC, RC20) Dataset with Identified Metabolites We used 76 clear cell renal cell carcinoma (ccRCC) samples, 24 normal and 52 tumor (Golkaram et al. 2022; Tang et al. 2023; Benedetti et al. 2023) as a case study. diff --git a/inst/app/www/GetStarted.html b/inst/app/www/GetStarted.html index b98d195..7aa5f53 100644 --- a/inst/app/www/GetStarted.html +++ b/inst/app/www/GetStarted.html @@ -459,11 +459,18 @@

Preparing Data for Use with Our Tool

samples. -
-

Example data.

-

Two case studies are available to help you get started with iModMix. -You can use this data to run the application and explore its -features.

+
+

Example data

+

We provide ten multi-omic datasets (transcriptomics and metabolomics) +to further illustrate iModMix’s capabilities. These datasets (Benedetti +et al. 2023) have been formatted to meet iModMix specifications, with +variable columns labeled as “Feature_ID” and sample columns labeled as +“Samples”.

+

These datasets are readily accessible for download on Zenodo:
+https://doi.org/10.5281/zenodo.13988161

+

Furthermore, two case studies are available to help you get started +with iModMix. You can use this data to run the application and explore +its features.

Case Study 1. Clear cell renal cell carcinoma (ccRCC, RC20) Dataset with Identified Metabolites We used 76 clear cell renal cell carcinoma (ccRCC) samples, 24 normal and 52 tumor (Golkaram From 047f0f5320d7881f76b5feb02304efb287c45ee8 Mon Sep 17 00:00:00 2001 From: IsisNarvaez Date: Fri, 6 Mar 2026 11:54:38 -0500 Subject: [PATCH 5/7] Ignore R history file --- .gitignore | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index 73ff47d..bbb649a 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,4 @@ .Rproj.user /doc/ /Meta/ -*.Rproj \ No newline at end of file +*.Rproj.Rhistory From d5546042e77fa6820d19d621a192b32c4a154fc5 Mon Sep 17 00:00:00 2001 From: IsisNarvaez Date: Wed, 1 Apr 2026 10:28:31 -0400 Subject: [PATCH 6/7] "left" out --- .Rbuildignore | 2 ++ .Rhistory | 0 R/mod_module1.R | 6 ++++-- README.md | 14 ++++++++++++++ iModMix.Rproj | 18 ++++++++++++++++++ inst/app/www/IModMix_Documentation.Rmd | 6 ++++-- inst/app/www/IModMix_Documentation.html | 13 ++++++++----- 7 files changed, 50 insertions(+), 9 deletions(-) create mode 100644 .Rbuildignore create mode 100644 .Rhistory create mode 100644 iModMix.Rproj diff --git a/.Rbuildignore b/.Rbuildignore new file mode 100644 index 0000000..91114bf --- /dev/null +++ b/.Rbuildignore @@ -0,0 +1,2 @@ +^.*\.Rproj$ +^\.Rproj\.user$ diff --git a/.Rhistory b/.Rhistory new file mode 100644 index 0000000..e69de29 diff --git a/R/mod_module1.R b/R/mod_module1.R index b46c588..b8b81c9 100644 --- a/R/mod_module1.R +++ b/R/mod_module1.R @@ -22,8 +22,9 @@ mod_module1_ui <- function(id) { ns <- NS(id) tagList( - - sidebarPanel( + + sidebarLayout( + sidebarPanel( width = 4, fileInput( @@ -1068,6 +1069,7 @@ mod_module1_ui <- function(id) { ) ) ) + ) } #' module1 Server Functions diff --git a/README.md b/README.md index c2f1d03..01d1174 100644 --- a/README.md +++ b/README.md @@ -4,6 +4,7 @@ output: pdf_document: default --- # IModMix Tutorial +[![DOI](https://img.shields.io/badge/DOI-10.1093/bioinformatics/btag030-blue)](https://doi.org/10.1093/bioinformatics/btag030) `iModMix` is a novel network-based approach that integrates multi-omics data, including metabolomics, proteomics, and transcriptomics data, into a unified network to unveil associations across various layers of omics data and reveal significant associations with phenotypes of interest. # Introduction @@ -183,3 +184,16 @@ If there are more than two levels, it compares one level against the others. Dots mark outliers and a legend is provided for the compared phenotypes. ![](https://github.com/user-attachments/assets/9cad9a8f-cec8-4723-b871-fe99344e3ee0) + +## Publication + +If you use **iModMix**, please cite: + +Narváez-Bandera I, Lui A, Mekonnen YA, Rubio V, Sulman N, Wilson C, Ackerman HD, Ospina OE, Gonzalez-Calderon G, Flores E, Li Q, Chen A, Fridley B, Stewart P. +**iModMix: Integrative Module Analysis for Multi-omics Data.** +*Bioinformatics*. 2026;42(2):btag030. +https://doi.org/10.1093/bioinformatics/btag030 + +Preprint: https://doi.org/10.1101/2024.11.12.623208 + +[Read the full publication](https://pubmed.ncbi.nlm.nih.gov/39605665/) diff --git a/iModMix.Rproj b/iModMix.Rproj new file mode 100644 index 0000000..eaa6b81 --- /dev/null +++ b/iModMix.Rproj @@ -0,0 +1,18 @@ +Version: 1.0 + +RestoreWorkspace: Default +SaveWorkspace: Default +AlwaysSaveHistory: Default + +EnableCodeIndexing: Yes +UseSpacesForTab: Yes +NumSpacesForTab: 2 +Encoding: UTF-8 + +RnwWeave: Sweave +LaTeX: pdfLaTeX + +BuildType: Package +PackageUseDevtools: Yes +PackageInstallArgs: --no-multiarch --with-keep.source +PackageRoxygenize: rd,collate,namespace diff --git a/inst/app/www/IModMix_Documentation.Rmd b/inst/app/www/IModMix_Documentation.Rmd index 2924e77..e913cf4 100644 --- a/inst/app/www/IModMix_Documentation.Rmd +++ b/inst/app/www/IModMix_Documentation.Rmd @@ -60,7 +60,9 @@ In summary, this application will allow the user to perform multi-omic integrati When using iModMix, please cite the following publication: -Narváez-Bandera, I., Lui, A., Mekonnen, Y. A., Rubio, V., Sulman, N., Wilson, C., Ackerman, H., Ospina, o., Gonzalez-Calderon1 , G., Flores, E., Li, Q., Chen, A., Fridley, B., & Stewart, P. (2024). iModMix: Integrative Module Analysis for Multi-omics Data. bioRxiv, 2024-11. +Narváez-Bandera I, Lui A, Mekonnen YA, Rubio V, Sulman N, Wilson C, Ackerman HD, Ospina OE, Gonzalez-Calderon G, Flores E, Li Q, Chen A, Fridley B, Stewart P. iModMix: Integrative Module Analysis for Multi-omics Data. bioRxiv [Preprint]. 2025 May 14:2024.11.12.623208. doi: 10.1101/2024.11.12.623208. Update in: Bioinformatics. 2026 Feb 3;42(2):btag030. +doi: 10.1093/bioinformatics/btag030. PMID: 39605665; PMCID: PMC11601443. -Read the full publication: https://www.biorxiv.org/content/biorxiv/early/2024/12/17/2024.11.12.623208.full.pdf +Read the full publication: +https://pubmed.ncbi.nlm.nih.gov/39605665/ diff --git a/inst/app/www/IModMix_Documentation.html b/inst/app/www/IModMix_Documentation.html index bb2d20f..9e443f8 100644 --- a/inst/app/www/IModMix_Documentation.html +++ b/inst/app/www/IModMix_Documentation.html @@ -439,11 +439,14 @@

What does this application do?

How to cite

When using iModMix, please cite the following publication:

-

Narváez-Bandera, I., Lui, A., Mekonnen, Y. A., Rubio, V., Sulman, N., -Wilson, C., Ackerman, H., Ospina, o., Gonzalez-Calderon1 , G., Flores, -E., Li, Q., Chen, A., Fridley, B., & Stewart, P. (2024). iModMix: -Integrative Module Analysis for Multi-omics Data. bioRxiv, 2024-11.

-

Read the full publication: https://www.biorxiv.org/content/biorxiv/early/2024/12/17/2024.11.12.623208.full.pdf

+

Narváez-Bandera I, Lui A, Mekonnen YA, Rubio V, Sulman N, Wilson C, +Ackerman HD, Ospina OE, Gonzalez-Calderon G, Flores E, Li Q, Chen A, +Fridley B, Stewart P. iModMix: Integrative Module Analysis for +Multi-omics Data. bioRxiv [Preprint]. 2025 May 14:2024.11.12.623208. +doi: 10.1101/2024.11.12.623208. Update in: Bioinformatics. 2026 Feb +3;42(2):btag030. doi: 10.1093/bioinformatics/btag030. PMID: 39605665; +PMCID: PMC11601443.

+

Read the full publication: https://pubmed.ncbi.nlm.nih.gov/39605665/

From 13d6225d4a0030476aac1e8ecc4af9db70c894b6 Mon Sep 17 00:00:00 2001 From: Isis Narvaez-Bandera <34428713+IsisNarvaez@users.noreply.github.com> Date: Wed, 1 Apr 2026 11:22:58 -0400 Subject: [PATCH 7/7] Update package version to 1.1.2 --- DESCRIPTION | 4 ---- 1 file changed, 4 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index d3257cd..b94fe9e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,10 +1,6 @@ Package: iModMix Title: Integrative Modules for Multi-Omics Data -<<<<<<< HEAD -Version: 1.1.1 -======= Version: 1.1.2 ->>>>>>> master Authors@R: c( person(given = "Isis", family = "Narvaez-Bandera",