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rstudio-server-conda
Run Rstudio Server in a conda environmentcontainerize-conda
Turn an existing conda environment into a Singularity containernbimporter
Import ipython notebooks as modulesgeos
Google Earth Overlay Server - display map overlays in Google Earthsnakemake_nextflow_wdl
simple comparison of snakemake, nextflow and cromwell/wdlnxfvars
Access nextflow variables from python scripts or notebookspython-ci-versioneer
Use github actions to autobump python versions (versioneer alternative)mapsources
Custom map sources for GEOS (MOBAC compatible)jukitty
Proof of concept for a console-based jupyter lab.reportsrender
Render HTML reports from parametrized jupyter notebooks or Rmarkdown documents.energymeter
Using a raspberry pi to monitor energy consumption in the housedask-on-slurm
Tutorial on how to run dask on a SLURM cluster.universal_analysis_pipeline
Nextflow-based pipeline to run and deploy reproducible analyses.bd_rhapsody_velocyto
Nextflow workflow to run velocyto.py on BD Rhapsody BAM filessingle-cell-preprocessing-figure
An overview of different single-cell processing paths (from counts to UMAP)nf-core-test-modules
Nextflow pipeline to run all tests from the nf-core-modules repository"scanpy_reproducibility
Demonstrate that UMAP and Leiden analysis is not reproducible between different cpu architectures.scanpy_helpers
My custom helper functions for scanpy-based single-cell analyses.single-cell-analysis-nf
(Semi-)automatization of scRNA-seq QC, filtering and normalization down to an initial clustering based on scanpy and nextflow. Attempts to implement Malte LΓΌcken's best practices: https://www.embopress.org/doi/full/10.15252/msb.20199416pygenesig
a framework to generate and validate tissue-specific gene signatures.microbio
Minimalist python framework for dealing with biological datasingle_cell_data_integration
rostlab-tbg
The Bioinformatics Game for Android and iOSli_et_al_cell_2018_melanoma_scrna
Forked from https://bitbucket.org/tanaylab/li_et_al_cell_2018_melanoma_scrnaapache-spark-presentation
short demonstration on how to use apache spark for data analysis.nextflow-notebook-pipeline
Example how to use nf-core/jupyternotebook and nf-core/rmarkdownnotebook modulesBioQC-GTEx-signatures
bioqc_geo
Supplementary material for "Tissue heterogeneity is prevalent in gene expression studies"quantiseq_in_r
run the quanTIseq deconvolution step on a gene expression matrix directly in Rfantom5-sig
Extracting cell specific gene signatures from FANTOM5Love Open Source and this site? Check out how you can help us