lmweber

BestPracticesST

'Best Practices for Spatial Transcriptomics Analysis with Bioconductor' online book

diffcyt

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

OSTA-book

Redirect link to Best Practices ST book

HDCytoData

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

nnSVG

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

locus-c

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

regsplice

R package for detection of differential exon usage in RNA-seq and exon microarray data

nnSVG-analyses

Scripts to reproduce analyses and figures in nnSVG paper

ggspavis

Visualization functions for spatial transcriptomics data in R

PHDS-data-visualization-2024

Code and data files for BU PHDS Data Visualization Workshop 2024

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)

academic-website-template-bs4

Academic Website Template in Bootstrap 4.

BestPracticesST-resources

Resources for 'Best Practices for Spatial Transcriptomics Analysis with Bioconductor' online book

BestPracticesST-testing

BiocBook-testing

BiocBook

BRISC-extensions

git-demo

Demo repository

globus

LIBD Globus Share Endpoints

lmweber.github.io

Code repository for my website

lmweber.github.io-resources

Resources repository for my website

planets

Planets repository

seminar-slides

PDF backups of current seminar slides

smoothclust

Method for segmentation of spatial domains with smooth boundaries and clustering in spatial transcriptomics

smoothclust-analyses

Analyses for spatial clustering algorithm

SpatialExperiment

SpatialExperimentIO

Read in Xenium, CosMx, and Vizgen data as Spatial or SingleCell Experiment object.

spatialLIBD

Code for the spatialLIBD R/Bioconductor package and shiny app

SVGs-exploratory

Exploratory analyses for nnSVG project (spatially variable genes)

Visium-data-preprocessing

Online book on data preprocessing for 10x Genomics Visium spatial transcriptomics data