README.md

In wenweixiong/VALERIE: Visualising Splicing at Single-Cell Resolution

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.

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

wenweixiong/VALERIE documentation built on Dec. 7, 2022, 4:15 a.m.