Maarten-vd-Sande's repositories
smoothed-particle-hydrodynamics
Basic implementation of smoothed-particle hydrodynamics (SPH) in Python.
voorbeeldRepo
Voorbeeld repository voor de minor programmeren.
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
atom
:atom: The hackable text editor
deepTools
Tools to process and analyze deep sequencing data.
fluff
Fluff is a Python package that contains several scripts to produce pretty, publication-quality figures for next-generation sequencing experiments.
genomepy
Download genomes the easy way.
gffread
GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
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.
jbrowse-components
Source code for JBrowse 2, a modern React-based genome browser
kb_python
A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
MultiQC_TestData
Test data for MultiQC. See https://github.com/ewels/MultiQC
OrthoFinder
Phylogenetic orthology inference for comparative genomics
pretty_html_table-feedstock
A conda-smithy repository for pretty_html_table.
pyranges
Performant Pythonic GenomicRanges
pysradb
Package for fetching metadata and downloading data from SRA/ENA/GEO
Rosalind-BioInformatics-Stronghold
Solutions to http://rosalind.info/problems/list-view/?location=bioinformatics-stronghold
scepia
Single Cell Epigenome-based Inference of Activity
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.
snakemake
This is the development home of the workflow management system Snakemake. For general information, see
snakemake-workflow-catalog
A statically generated catalog of available Snakemake workflows
snakemake-wrappers
This is the development home of the Snakemake wrapper repository, see
staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
Teaching-Presentations
Repository to store teaching materials