lmweber Goto Github PK

hdcytodata-example

R code to reproduce example in Figure 1 in our HDCytoData paper

jackson-periodontal-disease

Code and data to reproduce statistical analysis in Jackson et al. paper on equine periodontal disease

latex-templates

LaTeX template for preprints and supplementary information documents

list-of-papers

List of papers I am reading

lmweber.github.io

My website

locus-c

Analysis code for locus coeruleus (LC) spatial transcriptomics project

material

Links to materials for STA 426 Fall Semester 2018

nnsvg

nnSVG: scalable method to identify spatially variable genes (SVGs) in spatially-resolved transcriptomics data based on nearest-neighbor Gaussian processes (NNGPs)

nnsvg-analyses

Scripts to reproduce analyses in nnSVG paper

osta-book

Redirect link to Best Practices ST book

ostaworkshopbioc2021

Repository for OSTA workshop at Bioc2021 conference

pd1_analysis_cellcnn

Code to run CellCnn analyses in collaboration paper by Krieg et al. (2018), Nature Medicine

performant-statistical-computing

Course webpage for Performant Statistical Computing and Algoware Development

planets

Planets repository

r-novice-inflammation

Software Carpentry introduction to R for novices using inflammation data.

r-packages-build-commands

Pipeline of commands for building and checking R packages

regsplice

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

rnaseqworkflow

rtsne-example

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

scdiff_comparisons

Example scripts demonstrating scDiff (Simone Tiberi) with CyTOF data

seminar-slides

PDF backups of current seminar slides

snp-dmx-cancer

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

spatialexperiment

spatialexperiment-analysis

repo to explore spatial data in R/Bioconductor and Python

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

stexampledata

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