{
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  "Package": "scviR",
  "Date": "2025-05-02",
  "Title": "experimental inferface from R to scvi-tools",
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  "Description": "This package defines interfaces from R to scvi-tools.  A\nvignette works through the totalVI tutorial for analyzing\nCITE-seq data.  Another vignette compares outputs of Chapter 12\nof the OSCA book with analogous outputs based on totalVI\nquantifications. Future work will address other components of\nscvi-tools, with a focus on building understanding of\nprobabilistic methods based on variational autoencoders.",
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  "URL": "https://github.com/vjcitn/scviR",
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  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 13:00:13 UTC",
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  "Author": "Vincent Carey [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-4046-0063>)",
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      "topics": [
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    },
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      "source": "new_citeseq.Rmd",
      "filename": "new_citeseq.html",
      "title": "CITE-seq setup for scviR, 2025",
      "author": "Vince Carey stvjc at channing.harvard.edu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Acquire CITE-seq data from 10x human discovery platform (15k cells, 349 proteins)",
        "Use the scvi-tools approach to preprocessing",
        "Prepare for TOTALVI",
        "Train TOTALVI",
        "Session info"
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      "created": "2025-05-12 09:57:52",
      "modified": "2025-10-21 16:30:36",
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      "title": "Comparing totalVI and OSCA book CITE-seq analyses",
      "author": "OSCA book authors and Vincent J. Carey, stvjc at channing.harvard.edu",
      "engine": "knitr::rmarkdown",
      "headings": [
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        "Acquire software",
        "Obtain key data representations",
        "Assemble a SingleCellExperiment with totalVI outputs",
        "Acquire cell identities and batch labels",
        "Acquire quantifications and latent space positions",
        "Drop 5k data from all",
        "Label the rows of components",
        "Find common cell ids",
        "Build the totalVI SingleCellExperiment",
        "Reduce the chapter 12 dataset to the cells held in common",
        "Key outputs of the chapter 12 analysis",
        "Clustering and projection based on the ADT quantifications",
        "Cluster profiles based on averaging ADT quantities within clusters",
        "Marker expression patterns in mRNA-based sub-clusters of ADT-based clusters",
        "Graduated relationships between mRNA and surface protein expression",
        "Analogs to the chapter 12 findings, based on totalVI quantifications",
        "The Leiden clustering in UMAP projection",
        "Cluster profiles based on average ADT abundance, using denoised protein quantifications",
        "Concordance in ADT-based clustering between OSCA and totalVI",
        "Subcluster assessment for OSCA cluster \"3\"",
        "Graduated relationships between ADT and mRNA abundance as measured by totalVI",
        "Conclusions",
        "Session information"
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      "filename": "citeseq_tut.html",
      "title": "scvi-tools CITE-seq tutorial in R, using serialized tutorial components",
      "author": "Follows scvi-tools doc, Gayoso, Steier et al. DOI 10.1038/s41592-020-01050-x",
      "engine": "knitr::rmarkdown",
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        "Retrieval of fitted VAE",
        "Trace of (negative) ELBO values",
        "Normalized quantities",
        "UMAP projection of Leiden clustering in the totalVI latent space",
        "Protein abundances in projected clusters",
        "Conclusions",
        "Appendix: The VAE module",
        "Session information"
      ],
      "created": "2023-02-05 04:08:20",
      "modified": "2025-05-12 09:57:52",
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    {
      "source": "scviR.Rmd",
      "filename": "scviR.html",
      "title": "scviR: an R package interfacing Bioconductor and scvi-tools",
      "author": "Vince Carey stvjc at channing.harvard.edu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Installation and use",
        "Session information"
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      "created": "2023-01-26 20:53:41",
      "modified": "2025-05-12 09:57:52",
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