Software

Additional details are also available from GitHub.

nnSVG: R/Bioconductor package to identify spatially variable genes in spatial transcriptomics data (Weber et al. 2023).
SpatialExperiment: R/Bioconductor data structure for storing spatial transcriptomics datasets (Righelli, Weber, Crowell et al. 2022). (Joint project with Dario Righelli and Helena L. Crowell.)
ggspavis: R/Bioconductor package containing visualization functions for spatial transcriptomics data. (Joint project with Helena L. Crowell.)
diffcyt: R/Bioconductor package implementing a computational framework for differential discovery analyses in high-dimensional cytometry data (Weber et al. 2019).
regsplice: R/Bioconductor package implementing statistical methodology for detection of differential splicing (differential exon usage) in RNA sequencing data.

Orchestrating Spatial Transcriptomics Analysis with Bioconductor (OSTA): Online book providing code examples and discussion on computational analysis workflows for spatial transcriptomics data using R/Bioconductor.
CrispantCal: R/Shiny web application to calculate injection mix volumes for CRISPR-Cas9 experiments (described in: Burger et al. 2016).

WeberDivechaLCdata: R/Bioconductor package containing datasets from paper on analyses of single-nucleus and spatial transcriptomics data from the human locus coeruleus (Weber and Divecha et al. 2023).
STexampleData: R/Bioconductor package containing a collection of spatial transcriptomics datasets in SpatialExperiment Bioconductor format.
HDCytoData: R/Bioconductor package containing a collection of publicly available high-dimensional cytometry benchmark datasets in Bioconductor formats (Weber and Soneson, 2019).

locus-c: Code repository to reproduce analyses and figures in paper on analyzing spatial and single-nucleus data from the locus coeruleus (LC) region in the human brain (Weber and Divecha et al. 2023).
nnSVG-analyses: Code repository to reproduce analyses and figures in paper on the 'nnSVG' method (Weber et al. 2023).
snp-dmx-cancer: Snakemake pipeline and code repository to reproduce analyses and figures in paper evaluating genetic variation-based demultiplexing for single-cell RNA sequencing (Weber et al. 2021).
diffcyt-evaluations: Code repository to reproduce analyses and figures in paper introducing the 'diffcyt' framework (Weber et al. 2019).
cytometry-clustering-comparison: Code repository to reproduce analyses and figures in benchmark paper comparing clustering algorithms for high-dimensional cytometry data (Weber and Robinson, 2016).

FlowRepository FR-FCM-ZYL8: Data repository containing datasets used for benchmarking analyses in paper introducing the 'diffcyt' framework (Weber et al. 2019). These datasets are also provided in an easily accessible format in the 'HDCytoData' R/Bioconductor package.
FlowRepository FR-FCM-ZZPH: Data repository containing datasets used for benchmarking analyses in paper comparing clustering algorithms for high-dimensional cytometry data (Weber and Robinson, 2016). These datasets are also provided in an easily accessible format in the 'HDCytoData' R/Bioconductor package.