VALERIE

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# VALERIE
MARVEL is an R package developed for visualising alternative splicing events at single-cell resolution. It complements existing genome browser to enable visualising large number of samples (cells) and large number of splicing events typical of single-cell splicing experiments.

![](https://raw.githubusercontent.com/wenweixiong/VALERIE/master/inst/extdata/Cover_Figure.png)

# Installation
```
# Install VALERIE package
library(devtools)
install_github("wenweixiong/VALERIE")

# Load package
library(VALERIE)

# Launch vignette
??VALERIE
```

# Tutorial
A comprehensive tutorial for using VALERIE to visualise single-cell splicing events can be found here: https://wenweixiong.github.io/VALERIE

# Publication
We have published VALERIE in PLoS Computation Biology: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008195

# Version control
**1.x.x**  
The pioneer version.

**2.0.0**  
Previously, user can specify more than 1 splicing event to plot at a time. Now, user will specify only 1 splicing event to plot at a time. This will increase the speed of reading in the BAM files and also reduce the complexity of the internal codes.

**2.0.1**  
(1) Anderson-darling added as an option for statistical testing of PSI values at each nucleotide position. User can activate this option by specifying "ad" for the _method_ argument.  
(2) Included a feature to track the progress of reading in the BAM files, which is the rate-limiting step of VALERIE. Hence, user can estimate the time of completion for plotting a given splicing event. User can activate this feature by specifying _TRUE_ for the _track_ argument.  
(3)  Previously, an adjusted p-value of < 0.05 was considered statistically significant. Now, user can customise this threshold using the _sig.pval_ argument.

**2.1.1**  
(1) DTS (https://arxiv.org/pdf/2007.01360.pdf) added as an option for statistical testing of PSI values at each nucleotide position. User can activate this option by specifying "dts" for the _method_ argument.

**2.1.2**  
(1) Fixed bugs related to cell group and cell group color matching.
(2) Included option (_show.mean.ci=FALSE_) to not show 95% confidence interval for mean PSI plot. Default _show.mean.ci=TRUE_

VALERIE

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