Pinned Repositories
bioinfosummer
Tutorial for AMSI BioInfoSummer 2018
devcomvis
Visualization practical for DevCom
fluff
Fluff is a Python package that contains several scripts to produce pretty, publication-quality figures for next-generation sequencing experiments.
geo2fastq
Download FASTQ files from the SRA archive
GEOparse
Python library to access Gene Expression Omnibus Database (GEO)
gimmemotifs-manuscript
p53scan
p53scan & p63scan: search for the p53 or p63 motif
pita
Pipeline to improve transcript annotation based on RNA-seq and ChIP-seq data.
genomepy
genes and genomes at your fingertips
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.
simonvh's Repositories
simonvh/fluff
Fluff is a Python package that contains several scripts to produce pretty, publication-quality figures for next-generation sequencing experiments.
simonvh/bioinfosummer
Tutorial for AMSI BioInfoSummer 2018
simonvh/pita
Pipeline to improve transcript annotation based on RNA-seq and ChIP-seq data.
simonvh/GEOparse
Python library to access Gene Expression Omnibus Database (GEO)
simonvh/gimmemotifs-manuscript
simonvh/p53scan
p53scan & p63scan: search for the p53 or p63 motif
simonvh/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
simonvh/bioconda-recipes
Conda recipes for the bioconda channel.
simonvh/bioconda-utils
Utilities for building and managing bioconda recipes
simonvh/biothings_client.py
This is a generic Python client for BioThings APIs
simonvh/bokeh
Interactive Data Visualization in the browser, from Python
simonvh/bucketcache-feedstock
A conda-smithy repository for bucketcache.
simonvh/cargo-port
cache packages permanently
simonvh/dragonn
A toolkit to learn how to model and interpret regulatory sequence data using deep learning.
simonvh/facilitators-penalosa-ruiz
simonvh/intercode
simonvh/kerasR
R interface to the keras library
simonvh/maelstrom-poster
Maelstrom poster for RSG-DREAM 2016
simonvh/norns
Simple yaml-based config module
simonvh/numpy
The fundamental package for scientific computing with Python.
simonvh/pharmgkb
BioThings Studio tutorial
simonvh/psap
CLI interface for the PSAP classifier, Mierlo, G. van. Predicting protein condensate formation using machine learning (Manuscript in Preparation).
simonvh/pybedtools
Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)
simonvh/pyfaidx
Efficient pythonic random access to fasta subsequences
simonvh/pySCENIC
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-CEll regulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
simonvh/refgenconf
A python object for standardized reference genome assets.
simonvh/seaborn
Statistical data visualization in Python
simonvh/seq2science
Automated preprocessing of Next-Generation-Sequencing data, including full ATAC-seq, ChIP-seq, and RNA-seq workflows. Take a look at the docs: https://vanheeringen-lab.github.io/seq2science
simonvh/sklearn-contrib-lightning-feedstock
A conda-smithy repository for sklearn-contrib-lightning.
simonvh/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks