grst/fantom5-sig

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Created about 8 years ago
Updated about 5 years ago

grst/fantom5-sig

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Extracting cell specific gene signatures from FANTOM5

rstudio-server-conda

Run Rstudio Server in a conda environment

containerize-conda

Turn an existing conda environment into a Singularity container

nbimporter

Import ipython notebooks as modules

geos

Google Earth Overlay Server - display map overlays in Google Earth

snakemake_nextflow_wdl

simple comparison of snakemake, nextflow and cromwell/wdl

nxfvars

Access nextflow variables from python scripts or notebooks

python-ci-versioneer

Use github actions to autobump python versions (versioneer alternative)

mapsources

Custom map sources for GEOS (MOBAC compatible)

Jupyter Notebook

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 house

dask-on-slurm

Tutorial on how to run dask on a SLURM cluster.

Jupyter Notebook

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 files

single-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 Lücken's best practices: https://www.embopress.org/doi/full/10.15252/msb.20199416

Jupyter Notebook

pygenesig

a framework to generate and validate tissue-specific gene signatures.

microbio

Minimalist python framework for dealing with biological data

single_cell_data_integration

rostlab-tbg

The Bioinformatics Game for Android and iOS

li_et_al_cell_2018_melanoma_scrna

Forked from https://bitbucket.org/tanaylab/li_et_al_cell_2018_melanoma_scrna

apache-spark-presentation

short demonstration on how to use apache spark for data analysis.

Jupyter Notebook

nextflow-notebook-pipeline

Example how to use nf-core/jupyternotebook and nf-core/rmarkdownnotebook modules

BioQC-GTEx-signatures

bioqc_geo

Supplementary material for "Tissue heterogeneity is prevalent in gene expression studies"

Jupyter Notebook

quantiseq_in_r

run the quanTIseq deconvolution step on a gene expression matrix directly in R

minimal-nextflow-template

Template repo for minimal nextflow pipelines. Use this instead of manually submitting SGE jobs.