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LIMES Institute, University of Bonn
- @jsschrepping
Stars
Flow cytometry analysis workflow. The aim of this project is to provide an intuitive workflow for the analysis of high-dimensionality cytometry data in R.
Reproducibility repository accompanying Wilk, Lee, Wei, Parks, et al. "Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19" bioRxiv (2020).
Methods to compute Local Inverse Simpson's Index (LISI)
A single cell RNA-seq workflow, including highly variable gene analysis, cell type assignment and differential expression analysis.
R/shiny interface for interactive visualization of data in SummarizedExperiment objects
SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
RNA-seq workflow using STAR and DESeq2
A tool that allows to get UMI counts from a single cell protein assay
Scripts and Snakemake pipeline used in the EMBL-ABR webinar
A SingleCell RNASeq pre-processing snakemake workflow
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
Differential expression analysis for single-cell RNA-seq data.
Single-cell analysis in Python. Scales to >1M cells.