Title: Variational Approximation for Joint Survival and Marker Models
Description: Estimates joint marker (longitudinal) and
and survival (time-to-event) outcomes using variational approximations.
The package supports multivariate markers allowing for
correlated error terms and multiple types of survival outcomes which may be
left-truncated, right-censored, and recurrent. Time-varying fixed and
random covariate effects are supported along with non-proportional hazards.
LinkingTo: Rcpp, RcppArmadillo, RcppEigen, testthat, psqn (>= 0.3.0)
Imports: Rcpp, splines, utils, stats, SimSurvNMarker, psqn, Matrix,
Suggests: rmarkdown, knitr, testthat (>= 3.0.0), xml2, R.rsp

Title: Visualising Splicing at Single-Cell Resolution
Description: Alternative splicing produces a variety of different protein products from a given gene. 'VALERIE' enables visualisation of alternative splicing events from high-throughput single-cell RNA-sequencing experiments. 'VALERIE' computes percent spliced-in (PSI) values for user-specified genomic coordinates corresponding to alternative splicing events. PSI is the proportion of sequencing reads supporting the included exon/intron as defined by Shiozawa (2018) <doi:10.1038/s41467-018-06063-x>. PSI are inferred from sequencing reads data based on specialised infrastructures for representing and computing annotated genomic ranges by Lawrence (2013) <doi:10.1371/journal.pcbi.1003118>. Computed PSI for each single cell are subsequently presented in the form of a heatmap implemented using the 'pheatmap' package by Kolde (2010) <https://CRAN.R-project.org/package=pheatmap>. Board overview of the mean PSI difference and associated p-values across different user-defined groups of single cells are presented in the form of a line graph using the 'ggplot2' package by Wickham (2007) <https://CRAN.R-project.org/package=ggplot2>.
Imports: GenomicAlignments (>= 1.16.0), GenomicRanges (>= 1.32.0),
Packaged: 2020-02-03 03:19:57 UTC; seanwenweixiong

Description: Contains logic for cell-specific gene set scoring of single cell RNA sequencing data.