Software/Apps
Here is a list of software packages / interactive web applications / analysis code that I contribute to:
Software
ShinyCell
ShinyCell is an R package for making interactive Shiny-based web applications to visualise single-cell data.
GeneSwitches
GeneSwitches is an R package for identifying the precise order of gene expression changes over pseudotime in single-cell data.
deltaTE
deltaTE is a set of R scripts for detecting translationally regulated genes via Ribo-seq and RNA-seq data.
Interactive Apps
ShinyCell: simple and sharable visualization of single-cell gene expression data
Example shiny apps for using the ShinyCell package to create interactive shiny apps to visualise and share single-cell data
Paper Example App 1 Example App 2
Modelling human blastocysts by reprogramming fibroblasts into iBlastoids
Shiny app for browsing scRNA-seq induced blastocyst organoids (iBlastoids) derived from reprogramming human dermal fibroblasts
Reprogramming roadmap reveals route to human induced trophoblast stem cells
Shiny app for browsing scRNA-seq, bulk RNA-seq and bulk ATAC-seq for reprogramming human dermal fibroblasts into primed / naive iPSCs.
A single-cell atlas of entorhinal cortex from individuals with Alzheimer’s disease reveals cell-type-specific gene expression regulation
Shiny app for browsing scRNA-seq of entorhinal cortex tissue from AD and healthy individuals.
Deposited Code
Reprogramming roadmap reveals route to human induced trophoblast stem cells
Analysis code for analysing scRNA-seq, bulk RNA-seq and bulk ATAC-seq data for reprogramming human dermal fibroblasts into primed / naive iPSCs.