This book will guide you through the practical steps of the in-person tutorial IP2 for the ISMB/ECCB 2023 conference in Lyon named: Spatial transcriptomics data analysis: theory and practice. […] This book will guide you through the practical steps of the in-person tutorial IP2 for the ISMB/ECCB 2023 conference in Lyon named: “Spatial transcriptomics data analysis: theory and practice”. Recent technological advances have led to the application of RNA Sequencing in situ. This allows for whole-transcriptome characterisation, at approaching single-cell resolution, while retaining the spatial … Read more →

This is an introduction to using RUV-III-NB (Salim et al. 2022) for removing unwanted variations from single cell RNA sequencing data. […] This is an introduction to using RUV-III-NB for removing unwanted variation from single cell RNA sequencing data (Salim et al. 2022). The first section RUV-III-NB model below briefly explains the statistical methodology behind RUV-III-NB. Readers who are not interested in the methodology can move straight to Preliminary settings. RUV-III-NB models the raw count for gene (g) and cell (c), (y_{gc}), as Negative Binomial (NB), (y_{gc} \sim … Read more →

This section of the OMICS course will cover NGS sequencing from FASTQ reads to differential RNA analysis. The general workflow is shown above. We will use a dataset from Saccharomyces cereviseae. The bookdown version of these pages is published at this site … Read more →

Documentation describing my analyses of 16S rRNA sequencing data. […] My name is Rachael Lappan, and I am a PhD candidate at the University of Western Australia. The core of my PhD work is the Perth Otitis Media Microbiome (biOMe) study, where I work on the upper respiratory tract microbiome in children with recurrent acute otitis media (middle ear infections). The first stage of this research involved characterising the microbiome (by 16S rRNA gene sequencing) on samples from children with ear infections compared with samples from seemingly resistant healthy controls. The paper can be … Read more →