lmweber

BestPracticesST

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

cytometry-clustering-comparison

R scripts to reproduce analyses in our paper comparing clustering methods for high-dimensional cytometry data

deconvolution-papers

List of papers on deconvolution of cell types in bulk RNA-seq based on single-cell signatures

diffcyt

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

FlowSOM-Rtsne-example

Worked example showing how to cluster and visualize flow/mass cytometry data using FlowSOM and Rtsne

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)

nnSVG

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

nnSVG-analyses

Scripts to reproduce analyses and figures in nnSVG paper

Rtsne-example

Short example showing how to calculate and plot a 2D t-SNE projection from mass cytometry data in R

lmweber/BestPracticesST

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

lmweber/diffcyt

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

lmweber/OSTA-book

Redirect link to Best Practices ST book

lmweber/nnSVG

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

lmweber/HDCytoData

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

lmweber/locus-c

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

lmweber/regsplice

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

lmweber/ggspavis

Visualization functions for spatial transcriptomics data in R

lmweber/nnSVG-analyses

Scripts to reproduce analyses and figures in nnSVG paper

lmweber/PHDS-data-visualization-2024

Code and data files for BU PHDS Data Visualization Workshop 2024

lmweber/STexampleData

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

lmweber/WeberDivechaLCdata

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

lmweber/academic-website-template-bs4

Academic Website Template in Bootstrap 4.

lmweber/BestPracticesST-resources

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

lmweber/BestPracticesST-testing

lmweber/BiocBook-testing

BiocBook

lmweber/BRISC-extensions

lmweber/git-demo

Demo repository

lmweber/globus

LIBD Globus Share Endpoints

lmweber/lmweber.github.io

Code repository for my website

lmweber/lmweber.github.io-resources

Resources repository for my website

lmweber/planets

Planets repository

lmweber/seminar-slides

PDF backups of current seminar slides

lmweber/smoothclust

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

lmweber/smoothclust-analyses

Analyses for spatial clustering algorithm

lmweber/SpatialExperiment

lmweber/SpatialExperimentIO

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

lmweber/spatialLIBD

Code for the spatialLIBD R/Bioconductor package and shiny app

lmweber/SVGs-exploratory

Exploratory analyses for nnSVG project (spatially variable genes)

lmweber/Visium-data-preprocessing

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