From e640a0965540436110bf2997ebe5e67c13c149df Mon Sep 17 00:00:00 2001 From: rela-v Date: Sun, 31 Aug 2025 09:12:01 -0400 Subject: [PATCH 1/4] commented out peptides --- data.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data.qmd b/data.qmd index 1f25239..c4a45c6 100644 --- a/data.qmd +++ b/data.qmd @@ -311,7 +311,7 @@ combine_scores_patch <- function(df_rna = NULL, df_prot = NULL, df_kin = NULL, t combined_df <- combine_scores_patch(df_rna = data$rna, df_prot = data$protein, df_kin = data$kinase, - df_pep = data$peptide, + # df_pep = data$peptide, tf_kin = chea3_results) string_ppi <- generate_string_ppi(params$species) From 049828ba6d6c77dbd901773cc9643cf7b556253f Mon Sep 17 00:00:00 2001 From: rela <136220062+rela-v@users.noreply.github.com> Date: Wed, 11 Feb 2026 08:54:58 -0500 Subject: [PATCH 2/4] new gmt for human bader --- index.qmd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/index.qmd b/index.qmd index bd3ce4b..d9bef8d 100755 --- a/index.qmd +++ b/index.qmd @@ -6,8 +6,8 @@ date: last-modified date-format: "[Last Updated on] MMMM DD, YYYY" params: subtitle: "For Dr. XYZ" - species: rat # one of: [human, mouse, rat] - gmt: "https://download.baderlab.org/EM_Genesets/current_release/Rat/symbol/GO/Rat_GOALL_with_GO_iea_July_01_2024_symbol.gmt" + species: human # one of: [human, mouse, rat] + gmt: "https://download.baderlab.org/EM_Genesets/current_release/Human/symbol/Human_GO_AllPathways_noPFOCR_with_GO_iea_February_03_2026_symbol.gmt" data: value: # rna: "data/rna.csv" From 94f00cd0cf418ba00a21ec75bb434d3e96af3bb3 Mon Sep 17 00:00:00 2001 From: rela <136220062+rela-v@users.noreply.github.com> Date: Wed, 11 Feb 2026 14:36:56 -0500 Subject: [PATCH 3/4] all networks done --- index.qmd | 4 ++-- networks.qmd | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/index.qmd b/index.qmd index d9bef8d..cbe00aa 100755 --- a/index.qmd +++ b/index.qmd @@ -12,9 +12,9 @@ params: value: # rna: "data/rna.csv" # protein: "data/protein.csv" - kinase_stk: "data/creedenzymatic.csv" + kinase_stk: "data/kinase.csv" # kinase_ptk: "data/kinase.csv" - peptide: "data/dpp_file.csv" + peptide: "data/peptides.csv" --- This is a MultomicMenu report. diff --git a/networks.qmd b/networks.qmd index 5ce9405..7e22306 100644 --- a/networks.qmd +++ b/networks.qmd @@ -79,7 +79,7 @@ generate_seeded_network <- function(kinograte_res, gene, degree=1) { ``` ```{r} -genes_input <- names(combined) %>% sample(100) +genes_input <- combined %>% head(100) %>% names() plot <- generate_subnetwork(kinograte_res, genes_input) @@ -90,4 +90,4 @@ gene_input <- names(combined) %>% sample(1) plot <- generate_seeded_network(kinograte_res, gene_input, 1) plot -``` \ No newline at end of file +``` From df4aee5d55ab73ffa3bf51133dde2451fcc0af1e Mon Sep 17 00:00:00 2001 From: rela <136220062+rela-v@users.noreply.github.com> Date: Wed, 11 Feb 2026 15:02:05 -0500 Subject: [PATCH 4/4] added README.md --- README.md | 90 +++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 90 insertions(+) create mode 100644 README.md diff --git a/README.md b/README.md new file mode 100644 index 0000000..7b45e37 --- /dev/null +++ b/README.md @@ -0,0 +1,90 @@ +# ๐Ÿงฌ MultiomicMenu + +**Lead Scientist:** Dr. William G Ryan V +**Last Updated:** February 11, 2026 +**Status:** [Draft] + +This repository provides a standardized, configuration-driven framework for integrating high-dimensional multi-modal data (e.g., RNA-seq, Proteomics, etc.). The purpose of utilizing **Quarto (`.qmd`)** in this pipeline is to transform raw data into a fully documented, publication-ready HTML or PDF reports. + +--- + +## ๐Ÿš€ Quick Start + +You do not need to rewrite the analysis code. Follow these steps to generate your report: + +1. **Use the Template, Download, and Navigate to Folder:** + a. Navigate to [https://github.com/CogDisResLab/MultiomicMenu](https://github.com/CogDisResLab/MultiomicMenu) + b. Click "Use this template" on the upper right corner of the page. + c. Choose a name for your repository. Remember to make it private for sensitive data. + d. Use git clone on your new repository: + ```bash + git clone `git clone [https://github.com/](https://github.com/)[username]/[repo-name].git` + cd [repo-name] + ``` + +2. **Environment Setup:** + Open R in the project working directory and restore the required package versions: + ```r + if (!require("renv")) install.packages("renv") + renv::restore() + ``` +3. **Configure:** + Edit `index.qmd` with the following *important details*: + a. title + b. species + c. gmt (MUST be changed if not using human data) + d. data -> value -> data files +4. **Render:** + Execute the pipeline via the terminal: + ```bash + quarto render . + ``` +--- + +## ๐Ÿ“‚ Repository Structure + +* `index.qmd`: **The Single Source of Truth.** Define all hyperparameters and file paths here. +* `data/`: Put your DEGs, DPPs, DAPs, or DAKs here. +* `learn.qmd`: Nothing is altered here: this is for informational purposes. +* `data.qmd`: All data processing is done in this step, including integration and PPI generation using Kinograte. +* `pathways.qmd`: All pathway data is processed here using PAVER. +* `networks.qmd`: Network diagrams are generated here using igraph. + +--- + +## โš™๏ธ Configuration (`config.yaml`) + +The pipeline logic is controlled entirely by the `config.yaml` file. Common parameters include: + +| Parameter | Description | Default/Example | +| :--- | :--- | :--- | +| `title` | Title used in the final report headers. | `"MultiomicMenu Report"` | +| `species` | Species used in the experiment. | `[human, rat, or mouse]` | +| `gmt` | GMT file to use for pathway information. | `gmt: "https://download.baderlab.org/EM_Genesets/current_release/Human/symbol/Human_GO_AllPathways_noPFOCR_with_GO_iea_February_03_2026_symbol.gmt"` | +| `data` | Data files to use. | `["kinase_stk: 'data/kinase.csv'"]` | + +--- + +## ๐Ÿงช Statistical Framework + +The integration primarily utilizes **Prize Collecting Steiner Forest (PCSF)** analysis with a PPI graph. + +--- + +## ๐Ÿ›  Requirements + +* **R:** โ‰ฅ 4.5.0 +* **Quarto CLI:** System-level installation required ([Download](https://quarto.org/docs/get-started/)). +* **Memory:** 8GB+ RAM required. 16GB+ RAM recommended. + +--- + +## ๐Ÿ“Š Outputs + +Upon completion, the `results/` directory will contain: +1. **`index.html`**: An interactive report featuring all of the below pages. +2. **`learn.html`**: A page dedicated to describing the statistics and bioinformatics of MultiomicMenu. +3. **`data.html`**: A page for describing the data, including a "prize plot" which shows the cumulative distribution of "prizes". +4. **`pathways.html`**: A page for pathways that are hits in the analysis. +5. **`networks.html`**: A concatenation of all networks generated in the analysis, typically including a sample network and a seeded network. +