GitHub

Links to most of my software packages and code repositories are also available via GitHub.

Key packages and repositories are listed below. Additional smaller repositories are also available via GitHub.


Online book

  • OSTA: “Orchestrating Spatially Resolved Transcriptomics Analysis with Bioconductor”. Online textbook describing steps in a computational analysis pipeline for spatially resolved transcriptomics data, including example datasets and R code. Available from GitHub.

Software packages

  • diffcyt: R package implementing a computational framework for differential discovery analyses in high-dimensional cytometry data. Available from Bioconductor.

  • HDCytoData: R package providing streamlined access to a number of publicly available high-dimensional cytometry benchmark datasets in standard Bioconductor object formats. Available from Bioconductor.

  • regsplice: R package implementing statistical methodology for detection of differential splicing (differential exon usage) in RNA-seq data. Available from Bioconductor.


Code repositories


Data repositories

  • FlowRepository FR-FCM-ZYL8: Data repository containing datasets used in the benchmarking analyses from our paper introducing the diffcyt framework (Weber et al. 2019). These datasets are also provided in a more easily accessible format in the HDCytoData Bioconductor package.

  • FlowRepository FR-FCM-ZZPH: Data repository containing benchmark datasets from our paper comparing clustering algorithms for high-dimensional cytometry data (Weber and Robinson, 2016). These datasets are also provided in a more easily accessible format in the HDCytoData Bioconductor package.