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2016-05-30-zurich

Website for Data Carpentry workshop, University of Zurich, 30-31 May 2016

2019

Fall 2019 repository with course materials for JHU Advanced Data Science

academic-website-template-bs4

Academic Website Template in Bootstrap 4.

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

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

benchmarking-guidelines

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

bestpracticesst

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

bestpracticesst-resources

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

bestpracticesst-testing

biocbook-testing

BiocBook

biocstickers

Stickers for some Bioconductor packages - feel free to contribute and/or modify.

bookdown-demo

A minimal book example using bookdown

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

catalyst

Cytometry dATa anALYsis Tools

clustermatch

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

conference-slides-and-posters

Conference presentation slides and posters presented during my PhD

crispantcal

R/Shiny web app to calculate CRISPR-Cas9 injection mix volumes

cytof-example-data

CyTOF example data sets: BCR-XL

cytof-workshop-2017-03-13

Information and teaching materials for CyTOF workshop (R sessions), University of Zurich, 13-15 Mar 2017

cytof-workshop-2017-07-10

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

cytofworkflow

Package Homepage: http://bioconductor.org/packages/devel/bioc/html/cytofWorkflow.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=cytofWorkflow

cytometry-clustering-comparison

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

cytometry-perplexed

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

cytometry-trees

Cytometry clustering trees

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

diffcyt-evaluations

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