Bioinformatics Seminar
Time:
Venue: Na
18 July 2017
NaSingle-cells
Luke ZappiaMCRI
simulation and kidneys in a dish;Single-cell RNA sequencing (scRNA-seq) is rapidly becoming a tool of choice for biologists wishing to investigate gene expression at greater resolution ; particularly in areas such as development and differentiation. Single-cell data presents an array of bioinformatics challenges ; data is sparse (for both biological and technical reasons) ; quality control is difficult and it is unclear how to replicate measurements. As scRNA-seq datasets have become available so have a plethora of analysis methods. Evaluation of these methods relies on having a truth to test against or a deep biological knowledge to interpret the results. Unfortunately current scRNA-seq simulations are frequently poorly documented ; not reproducible and do not demonstrate similarity to real data or experimental designs. In this talk I will present Splatter ; a Bioconductor package for simulating scRNA-seq data that is designed to address these issues. Splatter provides a consistent ; easy to use interface to several previously published simulations allowing researchers to estimate parameters ; produce synthetic datasets and compare how well they replicate real data. Splatter also includes Splat ; our own simulation model. Based on a gamma-Poisson hierarchical model ; Splat includes additional features often seen in scRNA-Seq data ; such as dropout ; and can be used to simulate complex experiments including multiple cell types ; differentiation lineages and multiple batches. I will also discuss an analysis of a complex kidney organoid dataset ; showing how more cells and different levels of clustering help to reveal greater biological insight.;;