Gregor Sturm's repositories
rstudio-server-conda
Run Rstudio Server in a conda environment
containerize-conda
Turn an existing conda environment into a Singularity container
mapsources
Custom map sources for GEOS (MOBAC compatible)
bd_rhapsody_velocyto
Nextflow workflow to run velocyto.py on BD Rhapsody BAM files
minimal-nextflow-template
Template repo for minimal nextflow pipelines. Use this instead of manually submitting SGE jobs.
single-cell-preprocessing-figure
An overview of different single-cell processing paths (from counts to UMAP)
airr-standards
AIRR Community Data Standards
nextflow-notebook-pipeline
Example how to use nf-core/jupyternotebook and nf-core/rmarkdownnotebook modules
grst.github.io
jekyll repo for gregor-sturm.de
mMCPcounter
Murine version of MCP-counter, a tool to estimate the immune and stromal composition of heterogeneous tissue, from transcriptomic data
nf-rnaSeqMetagen
Metagenomics pipeline
ridge_significance
Ridge regression with a fast implementation of statistical significance test
scikit-bio
scikit-bio is an open-source, BSD-licensed, Python package providing data structures, algorithms, and educational resources for bioinformatics.
scverse.github.io
scverse.org website
scvi-criticism
Evaluation metrics for scvi-tools models
singularity-userdocs
User Documentation for SingularityCE.
sobolev_alignment
Sobolev alignment of deep probabilistic models for comparing single cell profiles
test-binder-conda-docker
Let's see if we can use different environments with binder