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qoiopipq merged 1 commit into from
Nov 10, 2025
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update links in vignettes/macpie.Rmd #143

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8 changes: 4 additions & 4 deletions vignettes/macpie.Rmd
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Expand Up @@ -31,8 +31,8 @@ MAC-seq is a cost-effective, high-throughput transcriptomic platform, developed
In this vignette we cover the basic functionality of <b>macpie</b>, 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
Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down