Simon Frerich's repositories
confuns
Convenience R functions
DEP
DEP package
Tangram
Spatial alignment of single cell transcriptomic data.
volcanoplot
Volcanoplot in Python
scanorama
Panoramic stitching of single cell data
scanpy-notebook-image
A repository for keeping conda env and docker image file for running single cell analysis using scanpy
scib
Benchmarking analysis of data integration tools
scib-pipeline
Snakemake pipeline that works with the scIB package to benchmark data integration methods.
SCINA
SCINA: A Semi-Supervised Subtyping Algorithm of Single Cells and Bulk Samples
seurat
R toolkit for single cell genomics
SPATA
SPATA Package for spatial gene expression analysis
SPATA2
A Toolbox for Spatial Gene Expression Analysis
squidpy
Spatial Single Cell Analysis in Python
TwoSampleMR
R package for performing 2-sample MR using MR-Base database
VISION
Signature Analysis and Visualization for Single-Cell RNA-seq
workshop-scRNAseq
Single cell RNA sequencing analysis course
workshop_omics_integration
Workshop in omics integration and systems biology