grst/jukitty

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Rank 1,807,489 (Top 36 %)
Language
Python
Created about 6 years ago
Updated over 3 years ago

grst/jukitty

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Proof of concept for a console-based jupyter lab.

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

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

fantom5-sig

Extracting cell specific gene signatures from FANTOM5

Jupyter Notebook

minimal-nextflow-template

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