Projects in Awesome Lists by lmweber

https://github.com/lmweber/cytometry-clustering-comparison

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

bioinformatics clustering comparison cytof flow-cytometry mass-cytometry single-cell

Last synced: 28 Oct 2024

https://github.com/lmweber/principlessta

"Principles of Spatial Transcriptomics Analysis with Bioconductor" book

analysis-workflows bioconductor spatial-transcriptomics spatially-resolved-transcriptomics

Last synced: 25 Oct 2024

https://github.com/lmweber/diffcyt

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

Last synced: 26 Oct 2024

https://github.com/lmweber/deconvolution-papers

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

Last synced: 06 Nov 2024

https://github.com/lmweber/flowsom-rtsne-example

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

Last synced: 28 Oct 2024

https://github.com/lmweber/rtsne-example

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

Last synced: 28 Oct 2024

https://github.com/lmweber/nnsvg

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

Last synced: 28 Oct 2024

https://github.com/lmweber/hdcytodata

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

Last synced: 28 Oct 2024

https://github.com/lmweber/benchmark-data-levine-32-dim

R code to prepare 32-dimensional CyTOF benchmark data set from Levine et al. (2015), for testing high-dimensional clustering algorithms

Last synced: 10 Oct 2024

https://github.com/lmweber/diffcyt-evaluations

Scripts to reproduce evaluations and figures in our paper introducing the 'diffcyt' framework

Last synced: 10 Oct 2024

https://github.com/lmweber/locus-c

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

Last synced: 06 Nov 2024

https://github.com/lmweber/pd1_analysis_cellcnn

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

Last synced: 06 Nov 2024

https://github.com/lmweber/snp-dmx-cancer

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

Last synced: 06 Nov 2024

https://github.com/lmweber/regsplice

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

Last synced: 28 Oct 2024

https://github.com/lmweber/cytof-workshop-2017-07-10

Information and teaching materials for CyTOF workshop (R sessions), University of Zurich, 10-12 July 2017

Last synced: 06 Nov 2024

https://github.com/lmweber/jackson-periodontal-disease

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

Last synced: 06 Nov 2024

https://github.com/lmweber/nnsvg-analyses

Scripts to reproduce analyses and figures in nnSVG paper

Last synced: 06 Nov 2024

https://github.com/lmweber/cytometry-trees

Cytometry clustering trees

Last synced: 06 Nov 2024

https://github.com/lmweber/ggspavis

Visualization functions for spatial transcriptomics data in R

Last synced: 28 Oct 2024

https://github.com/lmweber/stexampledata

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

Last synced: 06 Nov 2024

https://github.com/lmweber/clustermatch

R package for matching detected clusters to true clusters and evaluating performance

Last synced: 06 Nov 2024

https://github.com/lmweber/benchmark-data-levine-13-dim

R code to prepare 13-dimensional CyTOF benchmark data set from Levine et al. (2015), for testing high-dimensional clustering algorithms

Last synced: 06 Nov 2024

https://github.com/lmweber/smoothclust

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

Last synced: 10 Oct 2024

https://github.com/lmweber/useful-commands

Collection of useful commands and keyboard shortcuts for Mac and Linux

Last synced: 06 Nov 2024

https://github.com/lmweber/glmnet-error-example

Reproducible example to demonstrate possible bug in glmnet version 2.0-2

Last synced: 06 Nov 2024

https://github.com/lmweber/benchmarking-guidelines

Drafts of our review paper "Essential Practical Guidelines for Benchmarking Computational Methods"

Last synced: 06 Nov 2024

https://github.com/lmweber/cytometry-perplexed

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

Last synced: 06 Nov 2024

https://github.com/lmweber/weberdivechalcdata

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

Last synced: 06 Nov 2024

https://github.com/lmweber/phds-data-visualization-2024

Code and data files for BU PHDS Data Visualization Workshop 2024

Last synced: 06 Nov 2024

https://github.com/lmweber/hdcytodata-example

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

Last synced: 06 Nov 2024

https://github.com/lmweber/latex-templates

LaTeX template for preprints and supplementary information documents

Last synced: 06 Nov 2024

https://github.com/lmweber/osta-book

Redirect link to PrinciplesSTA book

Last synced: 06 Nov 2024

https://github.com/lmweber/seminar-slides

PDF backups of current seminar slides

Last synced: 06 Nov 2024

https://github.com/lmweber/scdiff_comparisons

Example scripts demonstrating scDiff (Simone Tiberi) with CyTOF data

Last synced: 06 Nov 2024

https://github.com/lmweber/material

Links to materials for STA 426 Fall Semester 2018

Last synced: 06 Nov 2024

https://github.com/lmweber/spatialexperiment-figures

Code to generate figures for SpatialExperiment paper

Last synced: 06 Nov 2024

https://github.com/lmweber/spatzli

R package containing functions for analyzing spatial transcriptomics data

Last synced: 06 Nov 2024

https://github.com/lmweber/r-packages-build-commands

Pipeline of commands for building and checking R packages

Last synced: 06 Nov 2024

https://github.com/lmweber/spkmedoids

R package implementing spatially weighted k-mediods algorithm

Last synced: 06 Nov 2024

https://github.com/lmweber/lmweber.github.io

Code repository for my website

Last synced: 06 Nov 2024

https://github.com/lmweber/bestpracticesst

Redirect link to PrinciplesSTA book

bioconductor spatial-transcriptomics spatially-resolved-transcriptomics

Last synced: 06 Nov 2024