Maarten-vd-Sande

ANANSE

Prediction of key transcription factors in cell fate determination using enhancer networks. See full ANANSE documentation for detailed installation instructions and usage examples. http://anansepy.readthedocs.io

lbm

Free-surface implementation of lattice boltzmann in Python.

qnorm

Fast-ish (and correct!) quantile normalization in Python.

smoothed-particle-hydrodynamics

Basic implementation of smoothed-particle hydrodynamics (SPH) in Python.

voorbeeldRepo

Voorbeeld repository voor de minor programmeren.

seq2science

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.

Maarten-vd-Sande/qnorm

Fast-ish (and correct!) quantile normalization in Python.

Maarten-vd-Sande/lbm

Free-surface implementation of lattice boltzmann in Python.

Maarten-vd-Sande/smoothed-particle-hydrodynamics

Basic implementation of smoothed-particle hydrodynamics (SPH) in Python.

Maarten-vd-Sande/voorbeeldRepo

Voorbeeld repository voor de minor programmeren.

Maarten-vd-Sande/ANANSE

Prediction of key transcription factors in cell fate determination using enhancer networks. See full ANANSE documentation for detailed installation instructions and usage examples. http://anansepy.readthedocs.io

Maarten-vd-Sande/atom

:atom: The hackable text editor

Maarten-vd-Sande/deepTools

Tools to process and analyze deep sequencing data.

Maarten-vd-Sande/fluff

Fluff is a Python package that contains several scripts to produce pretty, publication-quality figures for next-generation sequencing experiments.

Maarten-vd-Sande/genomepy

Download genomes the easy way.

Maarten-vd-Sande/gffread

GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more

Maarten-vd-Sande/gimmemotifs

Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed installation instructions and usage examples.

Maarten-vd-Sande/jbrowse-components

Source code for JBrowse 2, a modern React-based genome browser

Maarten-vd-Sande/kb_python

A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing

Maarten-vd-Sande/Maarten-vd-Sande

Maarten-vd-Sande/MultiQC

Aggregate results from bioinformatics analyses across many samples into a single report.

Maarten-vd-Sande/MultiQC_TestData

Test data for MultiQC. See https://github.com/ewels/MultiQC

Maarten-vd-Sande/OrthoFinder

Phylogenetic orthology inference for comparative genomics

Maarten-vd-Sande/pretty_html_table-feedstock

A conda-smithy repository for pretty_html_table.

Maarten-vd-Sande/pwmscan

Maarten-vd-Sande/pyranges

Performant Pythonic GenomicRanges

Maarten-vd-Sande/pysradb

Package for fetching metadata and downloading data from SRA/ENA/GEO

Maarten-vd-Sande/Rosalind-BioInformatics-Stronghold

Solutions to http://rosalind.info/problems/list-view/?location=bioinformatics-stronghold

Maarten-vd-Sande/scepia

Single Cell Epigenome-based Inference of Activity

Maarten-vd-Sande/seq2science

Automated preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and RNA-seq workflows. Works equally easy with public as local data.

Maarten-vd-Sande/snakemake

This is the development home of the workflow management system Snakemake. For general information, see

Maarten-vd-Sande/snakemake-workflow-catalog

A statically generated catalog of available Snakemake workflows

Maarten-vd-Sande/snakemake-wrappers

This is the development home of the Snakemake wrapper repository, see

Maarten-vd-Sande/staged-recipes

A place to submit conda recipes before they become fully fledged conda-forge feedstocks

Maarten-vd-Sande/Teaching-Presentations

Repository to store teaching materials