From abe82fd1ceac271390d9d42fb724691571f6cb30 Mon Sep 17 00:00:00 2001 From: ASintsova Date: Thu, 21 Mar 2024 21:14:39 +0100 Subject: [PATCH] Fixed links to the mbarq-app --- README.md | 2 +- docs/explore.md | 2 +- docs/index.rst | 2 +- docs/salmonella.md | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 54b3faf..7be3274 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ The main steps of the workflow involve: 1. Mapping each barcode to insertion location in the genome. 2. Profiling barcode abundances across samples. 3. Mutant fitness analyses. -4. Exploratory analysis using [mBARq web app]([https://mbarq-app.herokuapp.com/](https://microbiomics.io/tools/mbarq-app/)) +4. Exploratory analysis using [mBARq web app](https://microbiomics.io/tools/mbarq-app/) ## Installation: diff --git a/docs/explore.md b/docs/explore.md index fd1aef0..743ab83 100644 --- a/docs/explore.md +++ b/docs/explore.md @@ -1,7 +1,7 @@ # Explore -[mBARq Web App](https://mbarq-app.herokuapp.com/) allows quick and easy interactive exploration of your BarSeq experiment. +[mBARq Web App](https://microbiomics.io/tools/mbarq-app/) allows quick and easy interactive exploration of your BarSeq experiment. ## Visualise barcode positions across the genome diff --git a/docs/index.rst b/docs/index.rst index 9c552c2..66feace 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -21,7 +21,7 @@ The main steps of the workflow involve: 3. Mutant fitness analyses. 4. Exploratory analysis using `mBARq web app`_ -.. _mBARq web app: https://mbarq-app.herokuapp.com/ +.. _mBARq web app: https://microbiomics.io/tools/mbarq-app .. include:: install.md diff --git a/docs/salmonella.md b/docs/salmonella.md index 09e75ff..010bb7a 100644 --- a/docs/salmonella.md +++ b/docs/salmonella.md @@ -128,7 +128,7 @@ mkdir results mbarq analyze -i library_11_1_mbarq_merged_counts.csv -s sample_data.csv -c control_strains.csv --treatment_column day --baseline d0 -o results ``` -`mbarq analyze` creates a folder containing `library_11_1_mbarq_merged_counts_rra_results.csv` that lists log fold changes (LFC) and false discovery rates (FDR) for each gene in the library. You can upload this file to the [mBARq App](https://mbarq-app.herokuapp.com/) to create heatmaps, perform functional analysis, and visualize the results in the context of KEGG metabolic maps. +`mbarq analyze` creates a folder containing `library_11_1_mbarq_merged_counts_rra_results.csv` that lists log fold changes (LFC) and false discovery rates (FDR) for each gene in the library. You can upload this file to the [mBARq App](https://microbiomics.io/tools/mbarq-app/) to create heatmaps, perform functional analysis, and visualize the results in the context of KEGG metabolic maps.