grst

nxfvars

Access nextflow variables from python scripts or notebooks

python-ci-versioneer

Use github actions to autobump python versions (versioneer alternative)

pygenesig

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

scanpy_reproducibility

Demonstrate that UMAP and Leiden analysis is not reproducible between different cpu architectures.

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

bioqc_geo

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

benchmarking-transcriptomics-deconvolution

BioQC

Public version of ribiosBioQC

copykat

current-topics-bioinformatics-lecture

CytoSig

datascience-containers

Personal docker base images

harmony

Fast, sensitive and accurate integration of single-cell data with Harmony

ktplots

Some tools for plotting single-cell data

MOMF

multi-package-containers

Testing building mulled containers for multi-requirement tools.

nextflow

A DSL for data-driven computational pipelines

nextflow-module-dir-mounts

Reproducible example for nextflow not mounting moduleDir

nf-co.re

Code and files for the main nf-core website.

nf-deseq2

A RNA-seq differential expression analysis pipeline downstream of nf-core/rnaseq.

openmtbmap_openvelomap_linux

Linux script to extract and compile garmin *.img map files from openmtbmap.org or openvelomap.org downloads

podman-compose

a script to run docker-compose.yml using podman

progeny-py

PROGENY Python implementation

SCDC

SCDC

Scissor

Scissor package

shiny.router

A minimalistic router for your Shiny apps.

test_repo

testing some github actions permission issue

tidyHeatmap

Draw heatmap simply using a tidy data frame

tools

Python package with helper tools for the nf-core community.

vscode-jupytext