1. satuRn::Tasic_counts_vignette
    A 'Matrix' with transcript-level counts derived from our case study which builds on the dataset of Tasic et al. We used Salmon (V1.1.0) to quantify all L5IT cells (both for ALM and VISp tissue) from mice with a normal eye condition. From these cells, we randomly sampled 20 cells of each of the following cell types to use for this vignette; L5_IT_VISp_Hsd11b1_Endou, L5_IT_ALM_Tmem163_Dmrtb1 and L5_IT_ALM_Tnc. The data has already been leniently filtered with the 'filterByExpr' function of edgeR.
    csv| json| rda| rds
    matrix|22273 x 60
  2. satuRn::Tasic_metadata_vignette
    Metadata associated with the expression matrix 'Tasic_counts_vignette'. See '?Tasic_counts_vignette' for more information on the dataset.
    csv| xlsx| json| ndjson| rda| rds
    data.frame|60 x 3
  3. satuRn::sumExp_example
    A 'SummarizedExperiment' derived from our case study which builds on the dataset of Tasic et al. It contains the same cells as the data object used in the vignette (see '?Tasic_counts_vignette' for more information). In this SummarizedExperiment, we performed a filtering with 'filterByExpr' of edgeR with more stringent than default parameter settings (min.count = 100,min.total.count = 200, large.n = 50, min.prop = 0.9) to reduced the number of retained transcripts. We used this object to create an executable example in the help files of satuRn.
    rda| rds
    SummarizedExperiment