From 4fc433ac07a717f4c7486946581bd8d570802a28 Mon Sep 17 00:00:00 2001 From: Xin Liu Date: Mon, 24 Nov 2025 11:07:40 +1100 Subject: [PATCH] update README and links in vignettes --- README.Rmd | 26 +++++++++++++--------- README.md | 26 +++++++++++++--------- vignettes/cross_platform_compatibility.Rmd | 4 ++-- vignettes/macpie.Rmd | 3 +++ 4 files changed, 35 insertions(+), 24 deletions(-) diff --git a/README.Rmd b/README.Rmd index d475815..14036db 100644 --- a/README.Rmd +++ b/README.Rmd @@ -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} +#> } ``` diff --git a/README.md b/README.md index f69c1b2..37347a0 100644 --- a/README.md +++ b/README.md @@ -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} +#> } ``` diff --git a/vignettes/cross_platform_compatibility.Rmd b/vignettes/cross_platform_compatibility.Rmd index 61c8f02..ac1a423 100644 --- a/vignettes/cross_platform_compatibility.Rmd +++ b/vignettes/cross_platform_compatibility.Rmd @@ -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** @@ -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, diff --git a/vignettes/macpie.Rmd b/vignettes/macpie.Rmd index 0ce7639..27ccd9d 100644 --- a/vignettes/macpie.Rmd +++ b/vignettes/macpie.Rmd @@ -34,6 +34,9 @@ In this vignette we cover the basic functionality of macpie, 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