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update README and links in vignettes #144

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26 changes: 15 additions & 11 deletions README.Rmd
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Expand Up @@ -260,20 +260,24 @@ citation("macpie")
```r
#> To cite the macpie package in publications, please use:
#>
#> Bartonicek N, Liu X, Twomey L, Meier M, Lupat R, Craig S, Yoannidis D, Li J, Semple T,
#> Simpson K, Li M, Ramm S (2025). “macpie: a scalable workflow for high-throughput
#> transcriptomic profiling.” bioRxiv. doi:10.1101/2025.08.06.669002
#> Bartonicek N, Liu X, Twomey L, Meier M, Lupat R, Craig S, Yoannidis D, Li J, Semple T,
#> Simpson KJ, Li MX, Ramm S (2025). “macpie: a scalable workflow for high-throughput
#> transcriptomic profiling.” *Computational and Structural Biotechnology Journal*, 27. doi:10.1016/j.csbj.2025.11.002
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Article{,
#> title = {macpie: a scalable workflow for high-throughput transcriptomic profiling},
#> author = {Nenad Bartonicek and Xin Liu and Laura Twomey and Michelle Meier and Richard Lupat and Stuart Craig and David Yoannidis and Jason Li and Tim Semple and Kaylene J Simpson and Mark X Li and Susanne Ramm},
#> journal = {bioRxiv},
#> year = {2025},
#> doi = {10.1101/2025.08.06.669002},
#> url = {https://www.biorxiv.org/content/10.1101/2025.08.06.669002v1}
#> }
#> @Article{,
#> title = {macpie: a scalable workflow for high-throughput transcriptomic profiling},
#> journal = {Computational and Structural Biotechnology Journal},
#> year = {2025},
#> volume = {27},
#> doi = {10.1016/j.csbj.2025.11.002},
#> url = {https://www.sciencedirect.com/science/article/pii/S200103702500474X},
#> author = {Nenad Bartonicek and Xin Liu and Laura Twomey and Michelle Meier and Richard Lupat
#> and Stuart Craig and David Yoannidis and Jason Li and Tim Semple and Kaylene J Simpson
#> and Mark X Li and Susanne Ramm},
#> keywords = {High-throughput transcriptomics, Plate-based screens, Data integration, Software}
#> }

```

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26 changes: 15 additions & 11 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -245,18 +245,22 @@ citation("macpie")
``` r
#> To cite the macpie package in publications, please use:
#>
#> Bartonicek N, Liu X, Twomey L, Meier M, Lupat R, Craig S, Yoannidis D, Li J, Semple T,
#> Simpson K, Li M, Ramm S (2025). “macpie: a scalable workflow for high-throughput
#> transcriptomic profiling.” bioRxiv. doi:10.1101/2025.08.06.669002
#> Bartonicek N, Liu X, Twomey L, Meier M, Lupat R, Craig S, Yoannidis D, Li J, Semple T,
#> Simpson KJ, Li MX, Ramm S (2025). “macpie: a scalable workflow for high-throughput
#> transcriptomic profiling.” *Computational and Structural Biotechnology Journal*, 27. doi:10.1016/j.csbj.2025.11.002
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Article{,
#> title = {macpie: a scalable workflow for high-throughput transcriptomic profiling},
#> author = {Nenad Bartonicek and Xin Liu and Laura Twomey and Michelle Meier and Richard Lupat and Stuart Craig and David Yoannidis and Jason Li and Tim Semple and Kaylene J Simpson and Mark X Li and Susanne Ramm},
#> journal = {bioRxiv},
#> year = {2025},
#> doi = {10.1101/2025.08.06.669002},
#> url = {https://www.biorxiv.org/content/10.1101/2025.08.06.669002v1}
#> }
#> @Article{,
#> title = {macpie: a scalable workflow for high-throughput transcriptomic profiling},
#> journal = {Computational and Structural Biotechnology Journal},
#> year = {2025},
#> volume = {27},
#> doi = {10.1016/j.csbj.2025.11.002},
#> url = {https://www.sciencedirect.com/science/article/pii/S200103702500474X},
#> author = {Nenad Bartonicek and Xin Liu and Laura Twomey and Michelle Meier and Richard Lupat
#> and Stuart Craig and David Yoannidis and Jason Li and Tim Semple and Kaylene J Simpson
#> and Mark X Li and Susanne Ramm},
#> keywords = {High-throughput transcriptomics, Plate-based screens, Data integration, Software}
#> }
```
4 changes: 2 additions & 2 deletions vignettes/cross_platform_compatibility.Rmd
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Expand Up @@ -28,7 +28,7 @@ This vignette will cover the following two parts:

- Validating the metadata format and content.

- Some basic QC steps from [QC vignette](articles/quality_control.html).
- Some basic QC steps from [QC vignette](quality_control.html).


**2. Converting multiple DRUGseq plates**
Expand Down Expand Up @@ -717,7 +717,7 @@ plates <- c("VH02012942", "VH02012944", "VH02012956")
results <- lapply(plates, function(plate) {
select_robust_controls(
mac_filtered,
combined_id = "CB_43_EP73_0",
samples = "CB_43_EP73_0",
orig_ident = plate,
cpm_filter = 1,
min_samps = 8,
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3 changes: 3 additions & 0 deletions vignettes/macpie.Rmd
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Expand Up @@ -34,6 +34,9 @@ In this vignette we cover the basic functionality of <b>macpie</b>, from input,
- [Transcriptional analysis](transcriptional_analyses.html)
- [Compound screening](high_throughput_screens.html)
- [Cross-platform compatibility](cross_platform_compatibility.html)
- [Assessing sparsity](assessing_zero_inflation.html)
- [Working with Bioconductor classes](macpie_bioc.html)


### 1. Metadata import and QC

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