# Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications

## Documentation for package ‘satuRn’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

.StatModel | The StatModel class for satuRn
fitDTU | fitDTU
fitDTU-method | fitDTU
getCoef | Accessor functions for StatModel class
getCoef-method | Accessor functions for StatModel class
getDF | Accessor functions for StatModel class
getDF-method | Accessor functions for StatModel class
getDfPosterior | Accessor functions for StatModel class
getDfPosterior-method | Accessor functions for StatModel class
getDispersion | Accessor functions for StatModel class
getDispersion-method | Accessor functions for StatModel class
getModel | Accessor functions for StatModel class
getModel-method | Accessor functions for StatModel class
plotDTU | Plot function to visualize differential transcript usage (DTU)
StatModel | StatModel
StatModel-class | The StatModel class for satuRn
statModelAccessors | Accessor functions for StatModel class
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.
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.
Tasic_metadata_vignette | Metadata associated with the expression matrix 'Tasic_counts_vignette'. See '?Tasic_counts_vignette' for more information on the dataset.
testDTU | Test function to obtain a top list of transcripts that are differentially used in the contrast of interest