From 6f60f5c22dc55e43f2d86c3aefa59deea4bc73cc Mon Sep 17 00:00:00 2001 From: Xin Liu Date: Mon, 10 Nov 2025 14:47:33 +1100 Subject: [PATCH] update links in vignettes/macpie.Rmd --- vignettes/macpie.Rmd | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/vignettes/macpie.Rmd b/vignettes/macpie.Rmd index a0545e9..0ce7639 100644 --- a/vignettes/macpie.Rmd +++ b/vignettes/macpie.Rmd @@ -31,8 +31,8 @@ MAC-seq is a cost-effective, high-throughput transcriptomic platform, developed In this vignette we cover the basic functionality of macpie, from input, quality control to transcriptional and screen-related analyses. For more in-depth workflows, please refer to other vignettes: - [Quality control](quality_control.html) -- [Transcriptional analysis](transcriptional_analysis.html) -- [Compound screening](compound_screening.html) +- [Transcriptional analysis](transcriptional_analyses.html) +- [Compound screening](high_throughput_screens.html) - [Cross-platform compatibility](cross_platform_compatibility.html) ### 1. Metadata import and QC @@ -91,7 +91,7 @@ plot_metadata_heatmap(metadata) - use **plot_mds** to check sample grouping (umap/pca is also available using Seurat's functions) - use **compute_qc_metrics**, **plot_qc_metrics_heatmap**, and **plot_distance** to check sample variability and outliers - use **plot_rle** to check any row/column/plate effects and compare normalization methods - - more detailed methods avaailable in vignette [Quality control](articles/quality_control.html) + - more detailed methods available in vignette [Quality control](articles/quality_control.html) #### 2.1 Import data to tidySeurat object @@ -315,7 +315,7 @@ pheatmap(enriched_pathways_mat, color = macpie_colours$continuous_rev) gene expression or pathway enrichment - use **compute_multi_screen_profile** to find perturbations similar to your target profile or a known gene set - - more detailed methods avaailable in vignette [Compound screening](articles/compound_screening.html) + - more detailed methods available in vignette [Compound screening](articles/high_throughput_screens.html) #### 4.1. UMAP clustering based on DE genes