Gregor Sturm's repositories
rstudio-server-conda
Run Rstudio Server in a conda environment
mapsources
Custom map sources for GEOS (MOBAC compatible)
energymeter
Using a raspberry pi to monitor energy consumption in the house
nf-core-test-modules
Nextflow pipeline to run all tests from the nf-core-modules repository"
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).
cellcharter
A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
demultiplex
Demultiplexing pipeline for sequencing data
hiyapyco
HiYaPyCo - A Hierarchical Yaml Python Config
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
samshee
A schema-agnostic parser and writer for illumina® sample sheets v2 and similar documents.
scDblFinder
Methods for detecting doublets in single-cell sequencing data
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
wsireg
multimodal whole slide image registration in a graph structure