lmweber

diffcyt

R package for differential discovery analyses in high-dimensional cytometry data

OSTA-book

Redirect link to Best Practices ST book

nnSVG

nnSVG: scalable method to identify spatially variable genes (SVGs) in spatially-resolved transcriptomics data

HDCytoData

Data package containing high-dimensional cytometry data sets in SummarizedExperiment and flowSet formats

locus-c

Code to reproduce analyses in our paper on the landscape of gene expression in the human locus coeruleus (LC)

snp-dmx-cancer

Reproducible code for workflow and evaluations in our paper evaluating genetic variation-based demultiplexing tools in cancer

ggspavis

Visualization functions for spatial transcriptomics data in R

nnSVG-analyses

Scripts to reproduce analyses and figures in nnSVG paper

cytometry-perplexed

R scripts to generate figures in our paper Liechti et al. (2021)

STexampleData

Collection of spatially resolved transcriptomics datasets in SpatialExperiment R/Bioconductor format

WeberDivechaLCdata

Data package containing single-nucleus and spatially-resolved gene expression data from the human locus coeruleus (LC)

BRISC

Bootstrap for Rapid Inference on Spatial Covariances

BRISC-extensions

BRISC-extensions-analyses

Examples and documentation for our proposed extensions to BRISC for spatial transcriptomics data

bulk-gene-counts-HGSOC

Scripts for bulk RNA-seq gene count tables for HGSOC project

dmx-HGSOC-Dec2020-samples

Code to run demultiplexing on HGSOC samples from December 2020

list-of-papers

List of papers I am reading

lmweber.github.io

Code repository for my website

OSTAWorkshopBioc2021

Repository for OSTA workshop at Bioc2021 conference

performant-statistical-computing

Course webpage for Performant Statistical Computing and Algoware Development

planets

Planets repository

seminar-slides

PDF backups of current seminar slides

SpatialExperiment

SpatialExperiment-figures

Code to generate figures for SpatialExperiment paper

SpatialExperiment_Bioc2021

spatialLIBD

Code for the spatialLIBD R/Bioconductor package and shiny app

spatzli

R package containing functions for analyzing spatial transcriptomics data

spkmedoids

R package implementing spatially weighted k-mediods algorithm

SVGs-exploratory

Exploratory analyses for nnSVG project (spatially variable genes)

WorkshopTesting