Gregor Sturm's repositories
nf-core-test-modules
Nextflow pipeline to run all tests from the nf-core-modules repository"
simple-scvi
Example repo of using scvi-tools building blocks externally with simplified scVI implementation
spatialdata-plot
Static plotting for spatialdata
adjusttext-feedstock
A conda-smithy repository for adjusttext.
atlas_protocol
A computational protocol for atlas-level data integration and analysis as performed in Salcher et al. (2022).
cell2module
cell2module: gene module discovery from scRNA and scATAC using count-based Bayesian NMF
cellcharter
A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
easier
R package to use EaSIeR to predict anti-tumor immune response from bulk RNA-seq
fava
Functional Associations using Variational Autoencoders
infercnvpy
Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
MultiQC_TestData
Test data for MultiQC. See https://github.com/ewels/MultiQC
neutrophil-review
Code to generate figures for neutrophil review
nf-training-advanced
Customer workshop materials
Rfast
Fork of Rfast
scDblFinder
Methods for detecting doublets in single-cell sequencing data
scib-metrics
Accelerated, Python-only, single-cell integration benchmarking metrics
single-cell-best-practices
https://www.sc-best-practices.org
spatialtranscriptomics
Pipeline for processing spatially-resolved gene counts with spatial coordinates, image data, and optionally single cell RNA-seq data, designed for 10x genomics visium and single cell transcriptomics.
test-datasets
Test data to be used for automated testing with the nf-core pipelines
TSO500R
R package for data analysis with CombinedVariantOutput.tsv data